Starting phenix.real_space_refine on Thu Mar 5 20:43:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nku_12448/03_2026/7nku_12448.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nku_12448/03_2026/7nku_12448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nku_12448/03_2026/7nku_12448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nku_12448/03_2026/7nku_12448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nku_12448/03_2026/7nku_12448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nku_12448/03_2026/7nku_12448.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 120 5.16 5 B 6 2.79 5 C 15834 2.51 5 N 4344 2.21 5 O 4992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25332 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "B" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "C" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "D" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "E" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "F" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4143 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'AGS': 2, 'TDB': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'AGS': 2, 'TDB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'AGS': 2, 'TDB': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'AGS': 2, 'TDB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.98, per 1000 atoms: 0.24 Number of scatterers: 25332 At special positions: 0 Unit cell: (138.86, 136.74, 98.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 36 15.00 O 4992 8.00 N 4344 7.00 C 15834 6.00 B 6 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 12 sheets defined 56.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.597A pdb=" N ILE A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.697A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.815A pdb=" N MET A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.669A pdb=" N THR A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 499 removed outlier: 4.174A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 538 through 545 Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 592 through 608 Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 627 through 645 removed outlier: 3.940A pdb=" N SER A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 634 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N HIS A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.895A pdb=" N LEU A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 739 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.663A pdb=" N PHE A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 776 removed outlier: 3.632A pdb=" N ARG A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.513A pdb=" N ILE B 315 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 337 removed outlier: 3.630A pdb=" N THR B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 415 through 430 removed outlier: 3.695A pdb=" N MET B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.534A pdb=" N THR B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 499 removed outlier: 4.420A pdb=" N ASP B 497 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG B 499 " --> pdb=" O MET B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 538 Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 563 through 573 Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.689A pdb=" N ASN B 588 " --> pdb=" O PRO B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 608 removed outlier: 3.532A pdb=" N SER B 594 " --> pdb=" O TYR B 590 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 595 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 621 Processing helix chain 'B' and resid 628 through 645 removed outlier: 3.607A pdb=" N ALA B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 666 through 670 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.550A pdb=" N GLY B 706 " --> pdb=" O GLU B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 removed outlier: 3.938A pdb=" N LEU B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 739 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.532A pdb=" N PHE B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 776 Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 268 through 273 removed outlier: 3.671A pdb=" N SER C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 303 removed outlier: 3.553A pdb=" N LEU C 295 " --> pdb=" O GLY C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 removed outlier: 3.691A pdb=" N ILE C 315 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 337 removed outlier: 3.766A pdb=" N THR C 323 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA C 325 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 350 Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 415 through 430 removed outlier: 3.574A pdb=" N MET C 430 " --> pdb=" O GLN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'C' and resid 454 through 476 removed outlier: 4.083A pdb=" N ASP C 476 " --> pdb=" O GLY C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 499 removed outlier: 4.218A pdb=" N ASP C 497 " --> pdb=" O SER C 493 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG C 499 " --> pdb=" O MET C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 534 Processing helix chain 'C' and resid 538 through 546 Processing helix chain 'C' and resid 563 through 573 Processing helix chain 'C' and resid 584 through 586 No H-bonds generated for 'chain 'C' and resid 584 through 586' Processing helix chain 'C' and resid 590 through 608 removed outlier: 4.022A pdb=" N GLU C 595 " --> pdb=" O VAL C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 621 Processing helix chain 'C' and resid 628 through 645 removed outlier: 4.857A pdb=" N ASN C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N HIS C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 650 Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 666 through 670 Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 708 through 716 removed outlier: 4.041A pdb=" N LEU C 712 " --> pdb=" O ASP C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 739 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.533A pdb=" N PHE C 750 " --> pdb=" O GLU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 776 Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 267 through 273 removed outlier: 4.432A pdb=" N PHE D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 311 through 315 removed outlier: 3.568A pdb=" N ILE D 315 " --> pdb=" O GLY D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 337 removed outlier: 3.661A pdb=" N THR D 323 " --> pdb=" O TYR D 319 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 350 Processing helix chain 'D' and resid 362 through 375 Processing helix chain 'D' and resid 415 through 430 removed outlier: 3.890A pdb=" N MET D 430 " --> pdb=" O GLN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.510A pdb=" N THR D 458 " --> pdb=" O GLY D 454 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP D 476 " --> pdb=" O GLY D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 499 removed outlier: 4.300A pdb=" N ASP D 497 " --> pdb=" O SER D 493 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG D 499 " --> pdb=" O MET D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 538 Proline residue: D 535 - end of helix Processing helix chain 'D' and resid 538 through 546 Processing helix chain 'D' and resid 563 through 573 Processing helix chain 'D' and resid 582 through 586 removed outlier: 3.820A pdb=" N GLU D 585 " --> pdb=" O LYS D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 608 removed outlier: 4.450A pdb=" N ALA D 597 " --> pdb=" O GLU D 593 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE D 598 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 621 Processing helix chain 'D' and resid 626 through 631 Processing helix chain 'D' and resid 632 through 645 Processing helix chain 'D' and resid 646 through 650 Processing helix chain 'D' and resid 661 through 665 Processing helix chain 'D' and resid 666 through 670 removed outlier: 3.521A pdb=" N LEU D 670 " --> pdb=" O ALA D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.588A pdb=" N GLY D 706 " --> pdb=" O GLU D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 removed outlier: 4.084A pdb=" N LEU D 712 " --> pdb=" O ASP D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 739 Processing helix chain 'D' and resid 746 through 757 removed outlier: 3.652A pdb=" N PHE D 750 " --> pdb=" O GLU D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 775 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 267 through 274 removed outlier: 4.180A pdb=" N PHE E 271 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 303 Processing helix chain 'E' and resid 311 through 315 removed outlier: 3.766A pdb=" N ILE E 315 " --> pdb=" O GLY E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 337 removed outlier: 3.939A pdb=" N ALA E 325 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 Processing helix chain 'E' and resid 362 through 375 Processing helix chain 'E' and resid 415 through 430 removed outlier: 3.798A pdb=" N MET E 430 " --> pdb=" O GLN E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'E' and resid 454 through 476 removed outlier: 4.324A pdb=" N ASP E 476 " --> pdb=" O GLY E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 499 removed outlier: 4.131A pdb=" N ASP E 497 " --> pdb=" O SER E 493 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG E 499 " --> pdb=" O MET E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 538 Proline residue: E 535 - end of helix Processing helix chain 'E' and resid 538 through 545 Processing helix chain 'E' and resid 563 through 573 Processing helix chain 'E' and resid 584 through 586 No H-bonds generated for 'chain 'E' and resid 584 through 586' Processing helix chain 'E' and resid 590 through 608 Processing helix chain 'E' and resid 618 through 621 Processing helix chain 'E' and resid 627 through 646 removed outlier: 3.942A pdb=" N SER E 631 " --> pdb=" O GLY E 627 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA E 632 " --> pdb=" O SER E 628 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN E 634 " --> pdb=" O THR E 630 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N HIS E 635 " --> pdb=" O SER E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 650 Processing helix chain 'E' and resid 661 through 665 Processing helix chain 'E' and resid 666 through 670 Processing helix chain 'E' and resid 685 through 697 Processing helix chain 'E' and resid 708 through 716 removed outlier: 3.948A pdb=" N LEU E 712 " --> pdb=" O ASP E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 739 Processing helix chain 'E' and resid 746 through 756 removed outlier: 3.508A pdb=" N PHE E 750 " --> pdb=" O GLU E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 776 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 268 through 273 Processing helix chain 'F' and resid 291 through 303 removed outlier: 3.548A pdb=" N LEU F 295 " --> pdb=" O GLY F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 315 removed outlier: 3.673A pdb=" N ILE F 315 " --> pdb=" O GLY F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 337 removed outlier: 4.116A pdb=" N ALA F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 350 Processing helix chain 'F' and resid 362 through 375 Processing helix chain 'F' and resid 415 through 430 removed outlier: 3.784A pdb=" N MET F 430 " --> pdb=" O GLN F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 448 Processing helix chain 'F' and resid 454 through 476 removed outlier: 3.575A pdb=" N THR F 458 " --> pdb=" O GLY F 454 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP F 476 " --> pdb=" O GLY F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 499 Processing helix chain 'F' and resid 521 through 532 Processing helix chain 'F' and resid 538 through 545 Processing helix chain 'F' and resid 563 through 573 Processing helix chain 'F' and resid 584 through 586 No H-bonds generated for 'chain 'F' and resid 584 through 586' Processing helix chain 'F' and resid 590 through 608 Processing helix chain 'F' and resid 618 through 621 Processing helix chain 'F' and resid 626 through 646 removed outlier: 3.536A pdb=" N THR F 630 " --> pdb=" O ASP F 626 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN F 634 " --> pdb=" O THR F 630 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS F 635 " --> pdb=" O SER F 631 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 636 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 650 Processing helix chain 'F' and resid 661 through 665 Processing helix chain 'F' and resid 685 through 697 Processing helix chain 'F' and resid 702 through 706 Processing helix chain 'F' and resid 708 through 716 removed outlier: 3.946A pdb=" N LEU F 712 " --> pdb=" O ASP F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 739 Processing helix chain 'F' and resid 746 through 757 Processing helix chain 'F' and resid 762 through 776 Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 4.338A pdb=" N ASP A 345 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER A 340 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE A 386 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 342 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA A 388 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 344 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 577 through 582 removed outlier: 6.751A pdb=" N ASN A 577 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE A 614 " --> pdb=" O ASN A 577 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 579 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP A 616 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 581 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY A 552 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.294A pdb=" N HIS B 306 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 343 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 308 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP B 345 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE B 310 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER B 340 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 386 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE B 342 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA B 388 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 344 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 580 through 582 removed outlier: 3.606A pdb=" N ASP B 616 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER B 611 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL B 656 " --> pdb=" O SER B 611 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 613 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ALA B 658 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE B 615 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY B 552 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE B 679 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 554 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.255A pdb=" N HIS C 306 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE C 343 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 308 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASP C 345 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE C 310 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER C 340 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 386 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE C 342 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA C 388 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 344 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY C 281 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 577 through 582 removed outlier: 6.400A pdb=" N SER C 611 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL C 656 " --> pdb=" O SER C 611 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE C 613 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ALA C 658 " --> pdb=" O ILE C 613 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 615 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY C 552 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.150A pdb=" N HIS D 306 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE D 343 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU D 308 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASP D 345 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE D 310 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER D 340 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE D 386 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE D 342 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA D 388 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE D 344 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE D 282 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 577 through 581 removed outlier: 6.389A pdb=" N SER D 611 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 656 " --> pdb=" O SER D 611 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 613 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA D 658 " --> pdb=" O ILE D 613 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE D 615 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY D 552 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.243A pdb=" N HIS E 306 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE E 343 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU E 308 " --> pdb=" O PHE E 343 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP E 345 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE E 310 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER E 340 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE E 386 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE E 342 " --> pdb=" O ILE E 386 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ALA E 388 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE E 344 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 580 through 582 removed outlier: 3.538A pdb=" N ASP E 616 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER E 611 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL E 656 " --> pdb=" O SER E 611 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE E 613 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA E 658 " --> pdb=" O ILE E 613 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE E 615 " --> pdb=" O ALA E 658 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY E 552 " --> pdb=" O ARG E 677 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE E 679 " --> pdb=" O GLY E 552 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU E 554 " --> pdb=" O ILE E 679 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 306 through 310 removed outlier: 6.161A pdb=" N HIS F 306 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE F 343 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU F 308 " --> pdb=" O PHE F 343 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP F 345 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE F 310 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER F 340 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE F 386 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE F 342 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA F 388 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE F 344 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE F 282 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 577 through 582 removed outlier: 6.380A pdb=" N SER F 611 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL F 656 " --> pdb=" O SER F 611 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE F 613 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA F 658 " --> pdb=" O ILE F 613 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE F 615 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY F 552 " --> pdb=" O ARG F 677 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 679 " --> pdb=" O GLY F 552 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU F 554 " --> pdb=" O ILE F 679 " (cutoff:3.500A) 1230 hydrogen bonds defined for protein. 3498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 8727 1.37 - 1.51: 7864 1.51 - 1.66: 8987 1.66 - 1.80: 163 1.80 - 1.95: 41 Bond restraints: 25782 Sorted by residual: bond pdb=" C14 TDB A 903 " pdb=" S1 TDB A 903 " ideal model delta sigma weight residual 1.717 1.868 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C14 TDB F 801 " pdb=" S1 TDB F 801 " ideal model delta sigma weight residual 1.717 1.868 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C14 TDB D 801 " pdb=" S1 TDB D 801 " ideal model delta sigma weight residual 1.717 1.867 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C14 TDB C 801 " pdb=" S1 TDB C 801 " ideal model delta sigma weight residual 1.717 1.867 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C14 TDB D 804 " pdb=" S1 TDB D 804 " ideal model delta sigma weight residual 1.717 1.866 -0.149 2.00e-02 2.50e+03 5.53e+01 ... (remaining 25777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 34837 4.52 - 9.03: 122 9.03 - 13.55: 13 13.55 - 18.07: 12 18.07 - 22.59: 2 Bond angle restraints: 34986 Sorted by residual: angle pdb=" C13 TDB D 804 " pdb=" B1 TDB D 804 " pdb=" O1 TDB D 804 " ideal model delta sigma weight residual 127.55 104.96 22.59 3.00e+00 1.11e-01 5.67e+01 angle pdb=" C13 TDB A 904 " pdb=" B1 TDB A 904 " pdb=" O1 TDB A 904 " ideal model delta sigma weight residual 127.55 105.30 22.25 3.00e+00 1.11e-01 5.50e+01 angle pdb=" O15 TDB D 801 " pdb=" S15 TDB D 801 " pdb=" O16 TDB D 801 " ideal model delta sigma weight residual 118.86 102.15 16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C13 TDB F 801 " pdb=" B1 TDB F 801 " pdb=" O1 TDB F 801 " ideal model delta sigma weight residual 127.55 110.88 16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O15 TDB C 801 " pdb=" S15 TDB C 801 " pdb=" O16 TDB C 801 " ideal model delta sigma weight residual 118.86 102.27 16.59 3.00e+00 1.11e-01 3.06e+01 ... (remaining 34981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 15472 33.37 - 66.74: 384 66.74 - 100.11: 27 100.11 - 133.48: 1 133.48 - 166.85: 10 Dihedral angle restraints: 15894 sinusoidal: 6552 harmonic: 9342 Sorted by residual: dihedral pdb=" CA ASN A 588 " pdb=" C ASN A 588 " pdb=" N LYS A 589 " pdb=" CA LYS A 589 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA GLU D 573 " pdb=" C GLU D 573 " pdb=" N SER D 574 " pdb=" CA SER D 574 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLU A 573 " pdb=" C GLU A 573 " pdb=" N SER A 574 " pdb=" CA SER A 574 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 15891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3094 0.058 - 0.115: 803 0.115 - 0.173: 114 0.173 - 0.231: 5 0.231 - 0.288: 4 Chirality restraints: 4020 Sorted by residual: chirality pdb=" CB ILE A 498 " pdb=" CA ILE A 498 " pdb=" CG1 ILE A 498 " pdb=" CG2 ILE A 498 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU B 457 " pdb=" CB LEU B 457 " pdb=" CD1 LEU B 457 " pdb=" CD2 LEU B 457 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU F 457 " pdb=" CB LEU F 457 " pdb=" CD1 LEU F 457 " pdb=" CD2 LEU F 457 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4017 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" B1 TDB D 804 " -0.269 2.00e-02 2.50e+03 2.93e-01 2.57e+03 pdb=" C12 TDB D 804 " -0.195 2.00e-02 2.50e+03 pdb=" C13 TDB D 804 " -0.145 2.00e-02 2.50e+03 pdb=" C14 TDB D 804 " 0.061 2.00e-02 2.50e+03 pdb=" C2 TDB D 804 " 0.150 2.00e-02 2.50e+03 pdb=" C7 TDB D 804 " -0.063 2.00e-02 2.50e+03 pdb=" C8 TDB D 804 " -0.106 2.00e-02 2.50e+03 pdb=" N1 TDB D 804 " -0.190 2.00e-02 2.50e+03 pdb=" N2 TDB D 804 " 0.033 2.00e-02 2.50e+03 pdb=" O1 TDB D 804 " 0.841 2.00e-02 2.50e+03 pdb=" S1 TDB D 804 " 0.169 2.00e-02 2.50e+03 pdb=" S15 TDB D 804 " -0.286 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B1 TDB A 904 " 0.265 2.00e-02 2.50e+03 2.92e-01 2.55e+03 pdb=" C12 TDB A 904 " 0.191 2.00e-02 2.50e+03 pdb=" C13 TDB A 904 " 0.140 2.00e-02 2.50e+03 pdb=" C14 TDB A 904 " -0.061 2.00e-02 2.50e+03 pdb=" C2 TDB A 904 " -0.147 2.00e-02 2.50e+03 pdb=" C7 TDB A 904 " 0.066 2.00e-02 2.50e+03 pdb=" C8 TDB A 904 " 0.107 2.00e-02 2.50e+03 pdb=" N1 TDB A 904 " 0.189 2.00e-02 2.50e+03 pdb=" N2 TDB A 904 " -0.032 2.00e-02 2.50e+03 pdb=" O1 TDB A 904 " -0.839 2.00e-02 2.50e+03 pdb=" S1 TDB A 904 " -0.168 2.00e-02 2.50e+03 pdb=" S15 TDB A 904 " 0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B1 TDB D 801 " -0.246 2.00e-02 2.50e+03 2.48e-01 1.84e+03 pdb=" C12 TDB D 801 " -0.173 2.00e-02 2.50e+03 pdb=" C13 TDB D 801 " -0.120 2.00e-02 2.50e+03 pdb=" C14 TDB D 801 " 0.058 2.00e-02 2.50e+03 pdb=" C2 TDB D 801 " 0.144 2.00e-02 2.50e+03 pdb=" C7 TDB D 801 " -0.057 2.00e-02 2.50e+03 pdb=" C8 TDB D 801 " -0.096 2.00e-02 2.50e+03 pdb=" N1 TDB D 801 " -0.147 2.00e-02 2.50e+03 pdb=" N2 TDB D 801 " 0.039 2.00e-02 2.50e+03 pdb=" O1 TDB D 801 " 0.694 2.00e-02 2.50e+03 pdb=" S1 TDB D 801 " 0.158 2.00e-02 2.50e+03 pdb=" S15 TDB D 801 " -0.255 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 316 2.57 - 3.15: 23355 3.15 - 3.73: 40711 3.73 - 4.32: 54502 4.32 - 4.90: 86162 Nonbonded interactions: 205046 Sorted by model distance: nonbonded pdb=" OG SER A 720 " pdb=" OE1 GLU A 723 " model vdw 1.986 3.040 nonbonded pdb=" OG SER D 720 " pdb=" OE1 GLU D 723 " model vdw 1.992 3.040 nonbonded pdb=" O2B AGS E 901 " pdb=" O2G AGS E 901 " model vdw 1.998 3.040 nonbonded pdb=" O2B AGS A 901 " pdb=" O3G AGS A 901 " model vdw 2.007 3.040 nonbonded pdb=" O2B AGS D 802 " pdb=" O2G AGS D 802 " model vdw 2.020 3.040 ... (remaining 205041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 239 through 780 or resid 902)) selection = (chain 'B' and (resid 239 through 780 or resid 902)) selection = (chain 'C' and (resid 239 through 780 or resid 802)) selection = (chain 'D' and (resid 239 through 780 or resid 802)) selection = (chain 'E' and (resid 239 through 780 or resid 902)) selection = (chain 'F' and (resid 239 through 780 or resid 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.430 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.151 25790 Z= 0.359 Angle : 0.941 22.586 34986 Z= 0.469 Chirality : 0.052 0.288 4020 Planarity : 0.011 0.293 4488 Dihedral : 15.331 166.853 9870 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3240 helix: 0.00 (0.13), residues: 1548 sheet: -0.10 (0.28), residues: 402 loop : -0.90 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 328 TYR 0.053 0.002 TYR C 444 PHE 0.024 0.002 PHE D 700 TRP 0.020 0.002 TRP F 515 HIS 0.011 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00752 (25782) covalent geometry : angle 0.94094 (34986) hydrogen bonds : bond 0.15613 ( 1230) hydrogen bonds : angle 6.51702 ( 3498) Misc. bond : bond 0.01510 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1040 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 VAL cc_start: 0.8921 (t) cc_final: 0.8663 (p) REVERT: A 333 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 335 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7803 (mtp-110) REVERT: A 408 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6677 (mt-10) REVERT: A 443 LYS cc_start: 0.8806 (mmpt) cc_final: 0.8277 (mmmm) REVERT: A 444 TYR cc_start: 0.8545 (t80) cc_final: 0.7989 (t80) REVERT: A 448 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7857 (mttp) REVERT: A 452 TYR cc_start: 0.7994 (m-80) cc_final: 0.7519 (m-80) REVERT: A 488 LEU cc_start: 0.8349 (tt) cc_final: 0.7967 (tp) REVERT: A 489 LYS cc_start: 0.8420 (mppt) cc_final: 0.8033 (mppt) REVERT: A 492 GLU cc_start: 0.7733 (mp0) cc_final: 0.7340 (mp0) REVERT: A 499 ARG cc_start: 0.6922 (tpm170) cc_final: 0.4572 (tpp-160) REVERT: A 512 LYS cc_start: 0.8365 (ttmm) cc_final: 0.8069 (ttpp) REVERT: A 513 VAL cc_start: 0.8820 (m) cc_final: 0.8357 (p) REVERT: A 514 TYR cc_start: 0.8541 (m-10) cc_final: 0.8322 (m-10) REVERT: A 523 GLU cc_start: 0.7370 (tp30) cc_final: 0.6920 (tp30) REVERT: A 540 GLU cc_start: 0.7316 (pp20) cc_final: 0.7067 (pp20) REVERT: A 548 SER cc_start: 0.8817 (m) cc_final: 0.8176 (p) REVERT: A 556 TYR cc_start: 0.8317 (p90) cc_final: 0.7963 (p90) REVERT: A 572 THR cc_start: 0.8409 (m) cc_final: 0.8186 (p) REVERT: A 582 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8064 (mmmm) REVERT: A 595 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7796 (mp0) REVERT: A 661 ARG cc_start: 0.7187 (mmm160) cc_final: 0.6823 (mmm160) REVERT: A 663 ASP cc_start: 0.7576 (p0) cc_final: 0.7107 (p0) REVERT: A 664 GLU cc_start: 0.7850 (pt0) cc_final: 0.7505 (pt0) REVERT: A 691 GLU cc_start: 0.8195 (tp30) cc_final: 0.7549 (tp30) REVERT: A 694 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8688 (mttp) REVERT: A 695 LYS cc_start: 0.8665 (tmtt) cc_final: 0.8313 (tptp) REVERT: A 698 LYS cc_start: 0.8980 (ptmm) cc_final: 0.8533 (ptpp) REVERT: A 717 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 730 GLU cc_start: 0.7769 (tp30) cc_final: 0.7561 (tp30) REVERT: A 751 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 752 LYS cc_start: 0.8725 (tttm) cc_final: 0.8357 (ttmm) REVERT: A 755 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8454 (ttmt) REVERT: A 770 GLU cc_start: 0.7384 (mp0) cc_final: 0.7129 (mp0) REVERT: B 252 LYS cc_start: 0.8255 (ttmm) cc_final: 0.8027 (ttmm) REVERT: B 262 GLU cc_start: 0.7790 (tp30) cc_final: 0.7459 (tp30) REVERT: B 266 HIS cc_start: 0.8176 (m-70) cc_final: 0.7662 (m170) REVERT: B 308 LEU cc_start: 0.8644 (mp) cc_final: 0.8068 (mp) REVERT: B 328 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7919 (ttm110) REVERT: B 333 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6612 (tm-30) REVERT: B 335 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7728 (mtp-110) REVERT: B 373 LEU cc_start: 0.8146 (tt) cc_final: 0.7911 (tt) REVERT: B 377 MET cc_start: 0.6840 (mpp) cc_final: 0.6558 (mpp) REVERT: B 421 ASP cc_start: 0.8219 (t0) cc_final: 0.7974 (t0) REVERT: B 444 TYR cc_start: 0.8494 (t80) cc_final: 0.8159 (t80) REVERT: B 463 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7841 (mm-30) REVERT: B 485 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8139 (mmtp) REVERT: B 488 LEU cc_start: 0.8494 (tp) cc_final: 0.8080 (tt) REVERT: B 492 GLU cc_start: 0.7751 (mp0) cc_final: 0.7511 (mp0) REVERT: B 493 SER cc_start: 0.8825 (t) cc_final: 0.8597 (p) REVERT: B 497 ASP cc_start: 0.7478 (t0) cc_final: 0.7054 (t0) REVERT: B 530 GLU cc_start: 0.7904 (tt0) cc_final: 0.7145 (tt0) REVERT: B 540 GLU cc_start: 0.7540 (pp20) cc_final: 0.7330 (pp20) REVERT: B 600 GLU cc_start: 0.7756 (pp20) cc_final: 0.7233 (pp20) REVERT: B 638 THR cc_start: 0.8589 (t) cc_final: 0.8206 (p) REVERT: B 642 ASN cc_start: 0.8319 (t0) cc_final: 0.8056 (t0) REVERT: B 643 GLU cc_start: 0.7902 (tp30) cc_final: 0.7616 (tp30) REVERT: B 661 ARG cc_start: 0.7448 (tpt170) cc_final: 0.6726 (tpt170) REVERT: B 664 GLU cc_start: 0.7892 (pt0) cc_final: 0.7585 (pt0) REVERT: B 680 TYR cc_start: 0.8686 (t80) cc_final: 0.8366 (t80) REVERT: B 694 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8696 (mtpp) REVERT: B 695 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8355 (tptp) REVERT: B 696 CYS cc_start: 0.8061 (t) cc_final: 0.7794 (t) REVERT: B 715 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7554 (ttp80) REVERT: B 717 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 751 GLU cc_start: 0.7688 (tm-30) cc_final: 0.6905 (tm-30) REVERT: B 752 LYS cc_start: 0.8684 (tttm) cc_final: 0.8317 (ttmm) REVERT: B 755 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8415 (ttmm) REVERT: C 255 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 262 GLU cc_start: 0.7859 (tp30) cc_final: 0.7620 (tp30) REVERT: C 292 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8641 (mttp) REVERT: C 308 LEU cc_start: 0.8780 (mp) cc_final: 0.8305 (mp) REVERT: C 333 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6673 (tm-30) REVERT: C 346 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7058 (mm-30) REVERT: C 382 LYS cc_start: 0.7186 (mtmt) cc_final: 0.6886 (mtmm) REVERT: C 391 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6995 (ptt90) REVERT: C 393 ASN cc_start: 0.8410 (m-40) cc_final: 0.8149 (m-40) REVERT: C 426 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8107 (mm-40) REVERT: C 453 VAL cc_start: 0.9075 (p) cc_final: 0.8747 (m) REVERT: C 467 LYS cc_start: 0.8422 (mttm) cc_final: 0.8214 (mmtp) REVERT: C 468 THR cc_start: 0.8560 (m) cc_final: 0.8031 (p) REVERT: C 493 SER cc_start: 0.8845 (t) cc_final: 0.8313 (p) REVERT: C 497 ASP cc_start: 0.7448 (t0) cc_final: 0.7195 (t0) REVERT: C 512 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7971 (mmmt) REVERT: C 522 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7375 (mm-30) REVERT: C 525 LYS cc_start: 0.8305 (tppp) cc_final: 0.8029 (tppp) REVERT: C 540 GLU cc_start: 0.7551 (pp20) cc_final: 0.7285 (pp20) REVERT: C 582 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8322 (mmmm) REVERT: C 595 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7805 (mt-10) REVERT: C 599 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7721 (mtt-85) REVERT: C 661 ARG cc_start: 0.7405 (tpt170) cc_final: 0.6493 (tpt90) REVERT: C 671 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.7886 (ttm-80) REVERT: C 691 GLU cc_start: 0.8165 (tp30) cc_final: 0.7737 (tp30) REVERT: C 751 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7343 (tm-30) REVERT: C 755 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8410 (tmtt) REVERT: C 770 GLU cc_start: 0.7471 (tp30) cc_final: 0.6971 (tp30) REVERT: C 774 LEU cc_start: 0.8945 (mm) cc_final: 0.8728 (mm) REVERT: D 247 VAL cc_start: 0.8774 (t) cc_final: 0.8541 (p) REVERT: D 252 LYS cc_start: 0.8264 (tppp) cc_final: 0.8053 (tppp) REVERT: D 254 ILE cc_start: 0.8886 (mm) cc_final: 0.8605 (mt) REVERT: D 292 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8408 (mttp) REVERT: D 297 ARG cc_start: 0.7012 (mmm160) cc_final: 0.6411 (mmm160) REVERT: D 301 ASN cc_start: 0.7438 (m110) cc_final: 0.7160 (m110) REVERT: D 308 LEU cc_start: 0.8548 (mp) cc_final: 0.8284 (mp) REVERT: D 328 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8045 (ttm110) REVERT: D 333 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6431 (tm-30) REVERT: D 426 GLN cc_start: 0.8417 (tp40) cc_final: 0.7913 (tp40) REVERT: D 443 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8458 (mmtp) REVERT: D 444 TYR cc_start: 0.8431 (t80) cc_final: 0.8118 (t80) REVERT: D 463 GLU cc_start: 0.8331 (tp30) cc_final: 0.8087 (tp30) REVERT: D 489 LYS cc_start: 0.8515 (mppt) cc_final: 0.8221 (mppt) REVERT: D 497 ASP cc_start: 0.7776 (t0) cc_final: 0.7563 (t0) REVERT: D 512 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7902 (ttmm) REVERT: D 517 ASP cc_start: 0.8547 (m-30) cc_final: 0.8339 (m-30) REVERT: D 523 GLU cc_start: 0.7478 (tp30) cc_final: 0.6843 (tp30) REVERT: D 542 PHE cc_start: 0.8845 (m-80) cc_final: 0.8618 (m-10) REVERT: D 551 LYS cc_start: 0.8200 (tppp) cc_final: 0.7937 (tppp) REVERT: D 556 TYR cc_start: 0.8250 (p90) cc_final: 0.7983 (p90) REVERT: D 563 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8309 (ttpt) REVERT: D 599 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7439 (mtt-85) REVERT: D 642 ASN cc_start: 0.8237 (t0) cc_final: 0.7840 (t0) REVERT: D 661 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6969 (tpt170) REVERT: D 687 ASN cc_start: 0.8550 (t0) cc_final: 0.8348 (t0) REVERT: D 699 LYS cc_start: 0.9166 (tptm) cc_final: 0.8951 (tppp) REVERT: D 715 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7854 (ttp-170) REVERT: D 717 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7294 (tm-30) REVERT: D 723 GLU cc_start: 0.7449 (mp0) cc_final: 0.6881 (mp0) REVERT: D 751 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7248 (tm-30) REVERT: D 752 LYS cc_start: 0.8775 (tptp) cc_final: 0.8351 (tptp) REVERT: D 755 LYS cc_start: 0.8729 (tttt) cc_final: 0.8421 (tptt) REVERT: D 770 GLU cc_start: 0.7690 (tp30) cc_final: 0.6855 (tp30) REVERT: D 774 LEU cc_start: 0.8793 (mm) cc_final: 0.8217 (mm) REVERT: E 297 ARG cc_start: 0.7189 (tpt90) cc_final: 0.6625 (tpt90) REVERT: E 308 LEU cc_start: 0.8572 (mp) cc_final: 0.8308 (mp) REVERT: E 444 TYR cc_start: 0.8383 (t80) cc_final: 0.8039 (t80) REVERT: E 448 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7999 (ttpt) REVERT: E 463 GLU cc_start: 0.8374 (tp30) cc_final: 0.8153 (tp30) REVERT: E 484 LEU cc_start: 0.7891 (mp) cc_final: 0.7609 (tp) REVERT: E 488 LEU cc_start: 0.8755 (tt) cc_final: 0.7927 (tp) REVERT: E 492 GLU cc_start: 0.7604 (mp0) cc_final: 0.7290 (mp0) REVERT: E 498 ILE cc_start: 0.7837 (tt) cc_final: 0.7578 (tt) REVERT: E 514 TYR cc_start: 0.8555 (m-10) cc_final: 0.8264 (m-10) REVERT: E 530 GLU cc_start: 0.7506 (tt0) cc_final: 0.7134 (tt0) REVERT: E 556 TYR cc_start: 0.8234 (p90) cc_final: 0.8029 (p90) REVERT: E 579 LEU cc_start: 0.8544 (mm) cc_final: 0.8122 (mm) REVERT: E 600 GLU cc_start: 0.7817 (pp20) cc_final: 0.7344 (pp20) REVERT: E 619 ASP cc_start: 0.7938 (m-30) cc_final: 0.7457 (m-30) REVERT: E 638 THR cc_start: 0.8568 (t) cc_final: 0.8291 (p) REVERT: E 642 ASN cc_start: 0.8417 (t0) cc_final: 0.8112 (t0) REVERT: E 695 LYS cc_start: 0.8611 (tmtt) cc_final: 0.8374 (tptp) REVERT: E 696 CYS cc_start: 0.8074 (t) cc_final: 0.7795 (t) REVERT: E 715 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7586 (ttp80) REVERT: E 723 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7704 (mm-30) REVERT: E 751 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 752 LYS cc_start: 0.8883 (tmtt) cc_final: 0.8436 (ttmm) REVERT: E 771 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7560 (tm-30) REVERT: F 308 LEU cc_start: 0.8517 (mp) cc_final: 0.8239 (mp) REVERT: F 310 ILE cc_start: 0.8652 (mt) cc_final: 0.8434 (mm) REVERT: F 333 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6979 (tm-30) REVERT: F 393 ASN cc_start: 0.8452 (m-40) cc_final: 0.8219 (m-40) REVERT: F 425 LYS cc_start: 0.8627 (mttm) cc_final: 0.8278 (mmmm) REVERT: F 448 LYS cc_start: 0.8389 (ttmm) cc_final: 0.8181 (ttmm) REVERT: F 468 THR cc_start: 0.8527 (m) cc_final: 0.8146 (p) REVERT: F 485 LYS cc_start: 0.8404 (mmtt) cc_final: 0.7935 (mmtt) REVERT: F 488 LEU cc_start: 0.8071 (tt) cc_final: 0.7703 (tt) REVERT: F 489 LYS cc_start: 0.8113 (mppt) cc_final: 0.7893 (mppt) REVERT: F 492 GLU cc_start: 0.7460 (mp0) cc_final: 0.7035 (mp0) REVERT: F 499 ARG cc_start: 0.7827 (tpm170) cc_final: 0.6562 (tpt170) REVERT: F 523 GLU cc_start: 0.7457 (tp30) cc_final: 0.7041 (tp30) REVERT: F 536 LEU cc_start: 0.8683 (mm) cc_final: 0.8483 (mt) REVERT: F 540 GLU cc_start: 0.7311 (pp20) cc_final: 0.7025 (pp20) REVERT: F 568 LYS cc_start: 0.8623 (mttt) cc_final: 0.8418 (mtpt) REVERT: F 595 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7763 (mm-30) REVERT: F 600 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7648 (tm-30) REVERT: F 642 ASN cc_start: 0.8445 (t0) cc_final: 0.8143 (t0) REVERT: F 661 ARG cc_start: 0.7417 (tpt170) cc_final: 0.6450 (tpt170) REVERT: F 663 ASP cc_start: 0.8284 (p0) cc_final: 0.7962 (p0) REVERT: F 676 ASP cc_start: 0.7657 (p0) cc_final: 0.7238 (p0) REVERT: F 687 ASN cc_start: 0.8797 (t0) cc_final: 0.8552 (t0) REVERT: F 691 GLU cc_start: 0.8205 (tp30) cc_final: 0.7798 (tp30) REVERT: F 729 GLN cc_start: 0.8541 (mt0) cc_final: 0.8237 (mt0) REVERT: F 730 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7669 (mm-30) REVERT: F 751 GLU cc_start: 0.7534 (tm-30) cc_final: 0.6988 (tm-30) REVERT: F 752 LYS cc_start: 0.8627 (tptp) cc_final: 0.8339 (tptp) REVERT: F 754 PHE cc_start: 0.8595 (t80) cc_final: 0.8375 (t80) REVERT: F 770 GLU cc_start: 0.7541 (tp30) cc_final: 0.6992 (tp30) outliers start: 0 outliers final: 0 residues processed: 1040 average time/residue: 0.1975 time to fit residues: 297.7608 Evaluate side-chains 954 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 954 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN D 267 GLN D 393 ASN F 301 ASN ** F 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.134316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111621 restraints weight = 43926.408| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.45 r_work: 0.3320 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25790 Z= 0.168 Angle : 0.738 12.889 34986 Z= 0.371 Chirality : 0.047 0.289 4020 Planarity : 0.006 0.111 4488 Dihedral : 13.439 156.092 3816 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.67 % Allowed : 13.15 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3240 helix: 0.66 (0.13), residues: 1548 sheet: 0.29 (0.29), residues: 348 loop : -0.63 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 775 TYR 0.026 0.002 TYR C 444 PHE 0.034 0.002 PHE D 587 TRP 0.010 0.002 TRP F 515 HIS 0.005 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00372 (25782) covalent geometry : angle 0.73841 (34986) hydrogen bonds : bond 0.04946 ( 1230) hydrogen bonds : angle 4.83936 ( 3498) Misc. bond : bond 0.00228 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 989 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.8148 (tp30) cc_final: 0.7583 (tm-30) REVERT: A 247 VAL cc_start: 0.8986 (t) cc_final: 0.8604 (p) REVERT: A 333 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 335 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8307 (mtp-110) REVERT: A 408 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 429 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8337 (mmm-85) REVERT: A 443 LYS cc_start: 0.8875 (mmpt) cc_final: 0.8410 (mmmm) REVERT: A 444 TYR cc_start: 0.8867 (t80) cc_final: 0.8384 (t80) REVERT: A 462 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8640 (ttm110) REVERT: A 485 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8067 (mmtt) REVERT: A 489 LYS cc_start: 0.8472 (mppt) cc_final: 0.8173 (mppt) REVERT: A 495 MET cc_start: 0.8709 (mtp) cc_final: 0.8436 (ttm) REVERT: A 499 ARG cc_start: 0.7055 (tpm170) cc_final: 0.6353 (tpm170) REVERT: A 512 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8479 (tttm) REVERT: A 513 VAL cc_start: 0.8882 (m) cc_final: 0.8281 (p) REVERT: A 514 TYR cc_start: 0.8705 (m-10) cc_final: 0.8344 (m-10) REVERT: A 523 GLU cc_start: 0.8096 (tp30) cc_final: 0.7349 (tp30) REVERT: A 530 GLU cc_start: 0.8073 (tt0) cc_final: 0.7857 (tt0) REVERT: A 540 GLU cc_start: 0.7929 (pp20) cc_final: 0.7483 (pp20) REVERT: A 548 SER cc_start: 0.8992 (m) cc_final: 0.8542 (p) REVERT: A 556 TYR cc_start: 0.8501 (p90) cc_final: 0.8093 (p90) REVERT: A 572 THR cc_start: 0.8752 (m) cc_final: 0.8472 (p) REVERT: A 582 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8476 (mmmm) REVERT: A 586 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 595 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8138 (mp0) REVERT: A 617 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 651 LYS cc_start: 0.9017 (tppt) cc_final: 0.8757 (tptp) REVERT: A 663 ASP cc_start: 0.8056 (p0) cc_final: 0.7630 (p0) REVERT: A 664 GLU cc_start: 0.8264 (pt0) cc_final: 0.8033 (pt0) REVERT: A 695 LYS cc_start: 0.8865 (tmtt) cc_final: 0.8552 (tptp) REVERT: A 698 LYS cc_start: 0.9145 (ptmm) cc_final: 0.8678 (ptpp) REVERT: A 701 ASN cc_start: 0.8277 (m-40) cc_final: 0.8064 (m-40) REVERT: A 717 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 730 GLU cc_start: 0.8471 (tp30) cc_final: 0.8117 (tp30) REVERT: A 737 MET cc_start: 0.7323 (ttm) cc_final: 0.7028 (ttm) REVERT: A 751 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7515 (tm-30) REVERT: A 752 LYS cc_start: 0.8927 (tttm) cc_final: 0.8546 (ttmm) REVERT: B 262 GLU cc_start: 0.8631 (tp30) cc_final: 0.8313 (tp30) REVERT: B 328 ARG cc_start: 0.8656 (ttm110) cc_final: 0.8293 (ttm110) REVERT: B 333 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7570 (tm-30) REVERT: B 421 ASP cc_start: 0.8836 (t0) cc_final: 0.8526 (t0) REVERT: B 434 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: B 448 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8476 (mtpt) REVERT: B 461 CYS cc_start: 0.8797 (t) cc_final: 0.8544 (t) REVERT: B 463 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8194 (mm-30) REVERT: B 486 VAL cc_start: 0.8916 (p) cc_final: 0.8653 (m) REVERT: B 490 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7971 (t0) REVERT: B 493 SER cc_start: 0.8908 (t) cc_final: 0.8609 (p) REVERT: B 497 ASP cc_start: 0.7987 (t0) cc_final: 0.7496 (t0) REVERT: B 512 LYS cc_start: 0.8454 (ttpp) cc_final: 0.8131 (ttpp) REVERT: B 525 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8443 (mmtp) REVERT: B 530 GLU cc_start: 0.8266 (tt0) cc_final: 0.7741 (tt0) REVERT: B 540 GLU cc_start: 0.8056 (pp20) cc_final: 0.7763 (pp20) REVERT: B 556 TYR cc_start: 0.8538 (p90) cc_final: 0.8300 (p90) REVERT: B 587 PHE cc_start: 0.8047 (t80) cc_final: 0.7565 (t80) REVERT: B 600 GLU cc_start: 0.8252 (pp20) cc_final: 0.7683 (pp20) REVERT: B 619 ASP cc_start: 0.8281 (m-30) cc_final: 0.8043 (m-30) REVERT: B 638 THR cc_start: 0.8590 (t) cc_final: 0.8213 (p) REVERT: B 641 LEU cc_start: 0.9088 (mt) cc_final: 0.8886 (mm) REVERT: B 642 ASN cc_start: 0.8769 (t0) cc_final: 0.8501 (t0) REVERT: B 643 GLU cc_start: 0.8754 (tp30) cc_final: 0.8389 (tp30) REVERT: B 661 ARG cc_start: 0.7084 (tpt170) cc_final: 0.5922 (tpm170) REVERT: B 689 ARG cc_start: 0.8859 (mtm-85) cc_final: 0.8658 (mtm-85) REVERT: B 694 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8599 (mtpp) REVERT: B 695 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8418 (tptm) REVERT: B 696 CYS cc_start: 0.8866 (t) cc_final: 0.8473 (t) REVERT: B 717 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 751 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 752 LYS cc_start: 0.8809 (tttm) cc_final: 0.8458 (ttmm) REVERT: B 755 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8395 (ttmm) REVERT: B 770 GLU cc_start: 0.8596 (tp30) cc_final: 0.8307 (mm-30) REVERT: B 775 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7496 (ttp80) REVERT: C 255 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 262 GLU cc_start: 0.8456 (tp30) cc_final: 0.8125 (tp30) REVERT: C 292 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8691 (mttm) REVERT: C 333 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7332 (tp30) REVERT: C 382 LYS cc_start: 0.7434 (mtmt) cc_final: 0.7156 (mtmm) REVERT: C 391 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7171 (ptt90) REVERT: C 393 ASN cc_start: 0.8665 (m-40) cc_final: 0.8421 (m-40) REVERT: C 406 ASP cc_start: 0.7370 (t0) cc_final: 0.6570 (m-30) REVERT: C 426 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8487 (mm110) REVERT: C 467 LYS cc_start: 0.8603 (mttm) cc_final: 0.8350 (mmtp) REVERT: C 490 ASP cc_start: 0.8553 (t0) cc_final: 0.7754 (t0) REVERT: C 493 SER cc_start: 0.8900 (t) cc_final: 0.8352 (p) REVERT: C 497 ASP cc_start: 0.8018 (t0) cc_final: 0.7759 (t0) REVERT: C 512 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8137 (mmmt) REVERT: C 522 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7927 (mm-30) REVERT: C 525 LYS cc_start: 0.8556 (tppp) cc_final: 0.8263 (tppp) REVERT: C 582 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8358 (mmmm) REVERT: C 595 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8123 (mt-10) REVERT: C 599 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.8237 (ttm-80) REVERT: C 600 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: C 671 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.7991 (ttm-80) REVERT: C 691 GLU cc_start: 0.8554 (tp30) cc_final: 0.8269 (tp30) REVERT: C 696 CYS cc_start: 0.8588 (t) cc_final: 0.8173 (p) REVERT: C 708 ASP cc_start: 0.8605 (p0) cc_final: 0.8124 (p0) REVERT: C 730 GLU cc_start: 0.8595 (tp30) cc_final: 0.7839 (mm-30) REVERT: C 751 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7806 (tm-30) REVERT: C 755 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8243 (tmtt) REVERT: C 771 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7345 (pp20) REVERT: D 247 VAL cc_start: 0.8819 (t) cc_final: 0.8514 (p) REVERT: D 252 LYS cc_start: 0.8647 (tppp) cc_final: 0.8341 (tppp) REVERT: D 254 ILE cc_start: 0.9070 (mm) cc_final: 0.8840 (mt) REVERT: D 301 ASN cc_start: 0.8307 (m110) cc_final: 0.7941 (m110) REVERT: D 328 ARG cc_start: 0.8896 (ttm110) cc_final: 0.8629 (ttm110) REVERT: D 333 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7174 (tm-30) REVERT: D 374 MET cc_start: 0.8336 (tpt) cc_final: 0.7937 (tpp) REVERT: D 410 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7983 (mm-30) REVERT: D 423 LEU cc_start: 0.9248 (mt) cc_final: 0.9000 (mt) REVERT: D 426 GLN cc_start: 0.8744 (tp40) cc_final: 0.8285 (tp40) REVERT: D 443 LYS cc_start: 0.8856 (mmtp) cc_final: 0.8514 (mmtp) REVERT: D 444 TYR cc_start: 0.8730 (t80) cc_final: 0.8207 (t80) REVERT: D 448 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8223 (ttmm) REVERT: D 461 CYS cc_start: 0.8632 (m) cc_final: 0.8184 (t) REVERT: D 463 GLU cc_start: 0.8675 (tp30) cc_final: 0.8411 (tp30) REVERT: D 489 LYS cc_start: 0.8583 (mppt) cc_final: 0.8211 (mppt) REVERT: D 492 GLU cc_start: 0.8523 (mp0) cc_final: 0.8259 (mp0) REVERT: D 497 ASP cc_start: 0.8441 (t0) cc_final: 0.8132 (t0) REVERT: D 512 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8120 (ttmm) REVERT: D 513 VAL cc_start: 0.8608 (m) cc_final: 0.8034 (p) REVERT: D 517 ASP cc_start: 0.8727 (m-30) cc_final: 0.8479 (m-30) REVERT: D 523 GLU cc_start: 0.8026 (tp30) cc_final: 0.7194 (tp30) REVERT: D 525 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8570 (mmmm) REVERT: D 556 TYR cc_start: 0.8371 (p90) cc_final: 0.8020 (p90) REVERT: D 599 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.7818 (mtt-85) REVERT: D 604 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8345 (ttmt) REVERT: D 638 THR cc_start: 0.8803 (t) cc_final: 0.8488 (p) REVERT: D 642 ASN cc_start: 0.8688 (t0) cc_final: 0.8341 (t0) REVERT: D 694 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8842 (mtmm) REVERT: D 699 LYS cc_start: 0.9216 (tptm) cc_final: 0.8935 (tppp) REVERT: D 715 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8245 (ttp-170) REVERT: D 717 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 723 GLU cc_start: 0.8275 (mp0) cc_final: 0.7490 (mp0) REVERT: D 751 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 755 LYS cc_start: 0.8835 (tttt) cc_final: 0.8472 (tptp) REVERT: D 770 GLU cc_start: 0.8222 (tp30) cc_final: 0.7219 (tp30) REVERT: E 253 GLU cc_start: 0.8279 (pm20) cc_final: 0.8038 (mp0) REVERT: E 297 ARG cc_start: 0.8274 (tpt90) cc_final: 0.7532 (tpt90) REVERT: E 306 HIS cc_start: 0.6577 (t70) cc_final: 0.6300 (t70) REVERT: E 311 ASN cc_start: 0.7942 (m-40) cc_final: 0.7726 (t0) REVERT: E 443 LYS cc_start: 0.8927 (tppt) cc_final: 0.8710 (tppt) REVERT: E 444 TYR cc_start: 0.8891 (t80) cc_final: 0.8352 (t80) REVERT: E 453 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8829 (m) REVERT: E 461 CYS cc_start: 0.8827 (m) cc_final: 0.8479 (t) REVERT: E 463 GLU cc_start: 0.8842 (tp30) cc_final: 0.8616 (tp30) REVERT: E 484 LEU cc_start: 0.8080 (mp) cc_final: 0.7831 (tp) REVERT: E 485 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8383 (mmtt) REVERT: E 488 LEU cc_start: 0.8721 (tt) cc_final: 0.7693 (tt) REVERT: E 490 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7886 (t0) REVERT: E 492 GLU cc_start: 0.8324 (mp0) cc_final: 0.7763 (mp0) REVERT: E 507 PHE cc_start: 0.6000 (p90) cc_final: 0.5752 (p90) REVERT: E 512 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8149 (ttpt) REVERT: E 556 TYR cc_start: 0.8522 (p90) cc_final: 0.8061 (p90) REVERT: E 600 GLU cc_start: 0.8296 (pp20) cc_final: 0.7806 (pp20) REVERT: E 619 ASP cc_start: 0.8279 (m-30) cc_final: 0.7895 (m-30) REVERT: E 642 ASN cc_start: 0.8595 (t0) cc_final: 0.8345 (t0) REVERT: E 661 ARG cc_start: 0.7085 (tpt90) cc_final: 0.6734 (tpt170) REVERT: E 663 ASP cc_start: 0.8943 (p0) cc_final: 0.8574 (p0) REVERT: E 664 GLU cc_start: 0.8409 (tt0) cc_final: 0.7912 (tt0) REVERT: E 691 GLU cc_start: 0.8534 (tp30) cc_final: 0.8121 (tp30) REVERT: E 695 LYS cc_start: 0.8688 (tmtt) cc_final: 0.8463 (tptm) REVERT: E 696 CYS cc_start: 0.8882 (t) cc_final: 0.8527 (t) REVERT: E 715 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.7550 (ttp80) REVERT: E 723 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8149 (mm-30) REVERT: E 745 VAL cc_start: 0.8380 (t) cc_final: 0.7756 (m) REVERT: E 752 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8461 (ttmm) REVERT: E 754 PHE cc_start: 0.8919 (t80) cc_final: 0.8190 (t80) REVERT: E 771 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7854 (tm-30) REVERT: F 240 GLU cc_start: 0.8284 (tp30) cc_final: 0.8069 (tp30) REVERT: F 308 LEU cc_start: 0.8962 (mp) cc_final: 0.8728 (mp) REVERT: F 310 ILE cc_start: 0.8771 (mt) cc_final: 0.8554 (mm) REVERT: F 333 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7557 (tm-30) REVERT: F 393 ASN cc_start: 0.8701 (m-40) cc_final: 0.8480 (m-40) REVERT: F 406 ASP cc_start: 0.7376 (t0) cc_final: 0.7041 (t0) REVERT: F 444 TYR cc_start: 0.8923 (t80) cc_final: 0.8283 (t80) REVERT: F 484 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8032 (mm) REVERT: F 485 LYS cc_start: 0.8537 (mmtt) cc_final: 0.7809 (mmtt) REVERT: F 490 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7912 (t0) REVERT: F 513 VAL cc_start: 0.8700 (m) cc_final: 0.8334 (p) REVERT: F 536 LEU cc_start: 0.8888 (mm) cc_final: 0.8530 (tp) REVERT: F 556 TYR cc_start: 0.8480 (p90) cc_final: 0.8124 (p90) REVERT: F 572 THR cc_start: 0.8585 (m) cc_final: 0.8226 (p) REVERT: F 573 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7669 (tm-30) REVERT: F 585 GLU cc_start: 0.7597 (pt0) cc_final: 0.7007 (pp20) REVERT: F 642 ASN cc_start: 0.8453 (t0) cc_final: 0.8139 (t0) REVERT: F 659 THR cc_start: 0.8625 (t) cc_final: 0.8374 (m) REVERT: F 661 ARG cc_start: 0.7137 (tpt170) cc_final: 0.6039 (tpt170) REVERT: F 663 ASP cc_start: 0.8483 (p0) cc_final: 0.7811 (p0) REVERT: F 676 ASP cc_start: 0.8039 (p0) cc_final: 0.7764 (p0) REVERT: F 687 ASN cc_start: 0.8838 (t0) cc_final: 0.8588 (t0) REVERT: F 691 GLU cc_start: 0.8584 (tp30) cc_final: 0.8220 (tp30) REVERT: F 723 GLU cc_start: 0.8336 (mp0) cc_final: 0.8127 (mt-10) REVERT: F 728 CYS cc_start: 0.8807 (m) cc_final: 0.8449 (m) REVERT: F 746 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7714 (mp0) REVERT: F 751 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7613 (tp30) REVERT: F 754 PHE cc_start: 0.8748 (t80) cc_final: 0.8520 (t80) outliers start: 45 outliers final: 21 residues processed: 1001 average time/residue: 0.1946 time to fit residues: 283.1532 Evaluate side-chains 951 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 922 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 443 LYS Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 285 HIS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 484 LEU Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 529 LYS Chi-restraints excluded: chain F residue 634 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 111 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 249 optimal weight: 0.0370 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN D 407 GLN D 687 ASN ** F 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.136485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114683 restraints weight = 44215.867| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.44 r_work: 0.3305 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25790 Z= 0.166 Angle : 0.696 12.418 34986 Z= 0.348 Chirality : 0.045 0.226 4020 Planarity : 0.006 0.077 4488 Dihedral : 13.040 156.567 3816 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.67 % Allowed : 16.44 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3240 helix: 0.87 (0.13), residues: 1554 sheet: 0.24 (0.30), residues: 354 loop : -0.52 (0.19), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 280 TYR 0.024 0.002 TYR C 444 PHE 0.035 0.002 PHE B 507 TRP 0.012 0.002 TRP C 515 HIS 0.025 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00370 (25782) covalent geometry : angle 0.69573 (34986) hydrogen bonds : bond 0.04402 ( 1230) hydrogen bonds : angle 4.54355 ( 3498) Misc. bond : bond 0.00131 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 956 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.8102 (tp30) cc_final: 0.7816 (tm-30) REVERT: A 335 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8402 (mtp-110) REVERT: A 408 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 429 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.8269 (mmm-85) REVERT: A 443 LYS cc_start: 0.8951 (mmpt) cc_final: 0.8672 (tppt) REVERT: A 444 TYR cc_start: 0.8807 (t80) cc_final: 0.8106 (t80) REVERT: A 448 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8181 (mtmm) REVERT: A 485 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8161 (mmtp) REVERT: A 488 LEU cc_start: 0.8189 (tp) cc_final: 0.7944 (tt) REVERT: A 492 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: A 495 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8416 (ttm) REVERT: A 512 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8364 (tttm) REVERT: A 514 TYR cc_start: 0.8662 (m-10) cc_final: 0.8339 (m-10) REVERT: A 523 GLU cc_start: 0.8222 (tp30) cc_final: 0.7469 (tp30) REVERT: A 530 GLU cc_start: 0.8130 (tt0) cc_final: 0.7855 (tt0) REVERT: A 540 GLU cc_start: 0.7970 (pp20) cc_final: 0.7522 (pp20) REVERT: A 548 SER cc_start: 0.8979 (m) cc_final: 0.8258 (p) REVERT: A 556 TYR cc_start: 0.8509 (p90) cc_final: 0.8175 (p90) REVERT: A 586 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8602 (tp) REVERT: A 595 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8311 (mt-10) REVERT: A 651 LYS cc_start: 0.9008 (tppt) cc_final: 0.8721 (tppt) REVERT: A 663 ASP cc_start: 0.8038 (p0) cc_final: 0.7358 (p0) REVERT: A 695 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8496 (tptp) REVERT: A 698 LYS cc_start: 0.9040 (ptmm) cc_final: 0.8568 (ptpp) REVERT: A 717 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 730 GLU cc_start: 0.8454 (tp30) cc_final: 0.8145 (tp30) REVERT: A 737 MET cc_start: 0.7457 (ttm) cc_final: 0.7170 (ttm) REVERT: A 751 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 752 LYS cc_start: 0.8951 (tttm) cc_final: 0.8555 (ttmm) REVERT: A 755 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8596 (ttmt) REVERT: B 311 ASN cc_start: 0.8053 (t0) cc_final: 0.7791 (t0) REVERT: B 324 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: B 328 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8313 (ttm110) REVERT: B 333 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 391 ARG cc_start: 0.8186 (ptt-90) cc_final: 0.7338 (ptt-90) REVERT: B 421 ASP cc_start: 0.8833 (t0) cc_final: 0.8469 (t0) REVERT: B 430 MET cc_start: 0.8481 (ptt) cc_final: 0.8217 (ptt) REVERT: B 448 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8480 (mtpt) REVERT: B 463 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8147 (mm-30) REVERT: B 486 VAL cc_start: 0.8965 (p) cc_final: 0.8719 (m) REVERT: B 490 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.7948 (t0) REVERT: B 493 SER cc_start: 0.8916 (t) cc_final: 0.8593 (p) REVERT: B 497 ASP cc_start: 0.8064 (t0) cc_final: 0.7569 (t0) REVERT: B 512 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8047 (ttpp) REVERT: B 525 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8165 (mmtt) REVERT: B 540 GLU cc_start: 0.8109 (pp20) cc_final: 0.7780 (pp20) REVERT: B 548 SER cc_start: 0.8857 (t) cc_final: 0.8522 (p) REVERT: B 556 TYR cc_start: 0.8575 (p90) cc_final: 0.8177 (p90) REVERT: B 585 GLU cc_start: 0.8296 (pt0) cc_final: 0.7605 (pp20) REVERT: B 587 PHE cc_start: 0.7999 (t80) cc_final: 0.7530 (t80) REVERT: B 600 GLU cc_start: 0.8238 (pp20) cc_final: 0.7731 (pp20) REVERT: B 617 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7630 (mp0) REVERT: B 619 ASP cc_start: 0.8402 (m-30) cc_final: 0.8165 (m-30) REVERT: B 638 THR cc_start: 0.8611 (t) cc_final: 0.8282 (p) REVERT: B 641 LEU cc_start: 0.9102 (mt) cc_final: 0.8892 (mm) REVERT: B 642 ASN cc_start: 0.8768 (t0) cc_final: 0.8487 (t0) REVERT: B 643 GLU cc_start: 0.8716 (tp30) cc_final: 0.8313 (tp30) REVERT: B 663 ASP cc_start: 0.8293 (p0) cc_final: 0.7907 (p0) REVERT: B 689 ARG cc_start: 0.8931 (mtm-85) cc_final: 0.8596 (mtm-85) REVERT: B 694 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8331 (mtpt) REVERT: B 695 LYS cc_start: 0.8686 (tmtt) cc_final: 0.8376 (tptm) REVERT: B 696 CYS cc_start: 0.8878 (t) cc_final: 0.8525 (t) REVERT: B 723 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 751 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7732 (tp30) REVERT: B 752 LYS cc_start: 0.8843 (tttm) cc_final: 0.8628 (ttmm) REVERT: B 755 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8463 (ttmm) REVERT: B 770 GLU cc_start: 0.8545 (tp30) cc_final: 0.8252 (mm-30) REVERT: C 253 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: C 255 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8133 (tm-30) REVERT: C 262 GLU cc_start: 0.8506 (tp30) cc_final: 0.8026 (tm-30) REVERT: C 267 GLN cc_start: 0.8924 (pt0) cc_final: 0.8656 (pt0) REVERT: C 324 GLU cc_start: 0.7554 (mp0) cc_final: 0.6673 (mp0) REVERT: C 333 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 382 LYS cc_start: 0.7387 (mtmt) cc_final: 0.7118 (mtmm) REVERT: C 393 ASN cc_start: 0.8744 (m-40) cc_final: 0.8483 (m-40) REVERT: C 410 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8015 (mm-30) REVERT: C 426 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8482 (mm-40) REVERT: C 467 LYS cc_start: 0.8672 (mttm) cc_final: 0.8274 (mmtp) REVERT: C 484 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8173 (mm) REVERT: C 488 LEU cc_start: 0.7758 (tp) cc_final: 0.7433 (tt) REVERT: C 490 ASP cc_start: 0.8524 (t0) cc_final: 0.7716 (t0) REVERT: C 492 GLU cc_start: 0.8409 (mp0) cc_final: 0.8178 (mp0) REVERT: C 493 SER cc_start: 0.8924 (t) cc_final: 0.8199 (p) REVERT: C 497 ASP cc_start: 0.8041 (t0) cc_final: 0.7790 (t0) REVERT: C 512 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8050 (mmmt) REVERT: C 522 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7901 (mm-30) REVERT: C 525 LYS cc_start: 0.8612 (tppp) cc_final: 0.8237 (tppp) REVERT: C 582 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8414 (mmmm) REVERT: C 595 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8016 (mt-10) REVERT: C 599 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.8409 (mtt-85) REVERT: C 600 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: C 661 ARG cc_start: 0.7246 (tpt170) cc_final: 0.6408 (tpt90) REVERT: C 663 ASP cc_start: 0.8643 (p0) cc_final: 0.8042 (p0) REVERT: C 666 ASP cc_start: 0.8372 (t0) cc_final: 0.7693 (p0) REVERT: C 671 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.7983 (ttm-80) REVERT: C 691 GLU cc_start: 0.8450 (tp30) cc_final: 0.8184 (tp30) REVERT: C 696 CYS cc_start: 0.8553 (t) cc_final: 0.8053 (p) REVERT: C 697 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8572 (t) REVERT: C 699 LYS cc_start: 0.9083 (tptm) cc_final: 0.8857 (tppt) REVERT: C 730 GLU cc_start: 0.8577 (tp30) cc_final: 0.8070 (mm-30) REVERT: C 737 MET cc_start: 0.7034 (mtt) cc_final: 0.6737 (mtt) REVERT: C 739 ASP cc_start: 0.7681 (t0) cc_final: 0.7481 (t0) REVERT: C 751 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 755 LYS cc_start: 0.8648 (tmtt) cc_final: 0.8268 (tmtt) REVERT: C 761 ILE cc_start: 0.8720 (tt) cc_final: 0.8380 (pt) REVERT: D 247 VAL cc_start: 0.8780 (t) cc_final: 0.8477 (p) REVERT: D 252 LYS cc_start: 0.8657 (tppp) cc_final: 0.8325 (tppp) REVERT: D 301 ASN cc_start: 0.8408 (m110) cc_final: 0.7984 (m110) REVERT: D 328 ARG cc_start: 0.8897 (ttm110) cc_final: 0.8580 (ttm110) REVERT: D 333 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 374 MET cc_start: 0.8364 (tpt) cc_final: 0.7935 (tpp) REVERT: D 426 GLN cc_start: 0.8837 (tp40) cc_final: 0.8369 (tp40) REVERT: D 443 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8482 (mmtp) REVERT: D 444 TYR cc_start: 0.8738 (t80) cc_final: 0.8347 (t80) REVERT: D 448 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8122 (ttmm) REVERT: D 461 CYS cc_start: 0.8665 (m) cc_final: 0.8214 (t) REVERT: D 463 GLU cc_start: 0.8661 (tp30) cc_final: 0.8127 (mm-30) REVERT: D 497 ASP cc_start: 0.8408 (t0) cc_final: 0.8151 (t70) REVERT: D 512 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8156 (ttmm) REVERT: D 513 VAL cc_start: 0.8465 (m) cc_final: 0.8213 (p) REVERT: D 523 GLU cc_start: 0.8032 (tp30) cc_final: 0.7211 (tp30) REVERT: D 525 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8675 (mmmm) REVERT: D 529 LYS cc_start: 0.8496 (tppp) cc_final: 0.7693 (tppt) REVERT: D 556 TYR cc_start: 0.8278 (p90) cc_final: 0.7977 (p90) REVERT: D 600 GLU cc_start: 0.8026 (pp20) cc_final: 0.7579 (pp20) REVERT: D 604 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8450 (ttmt) REVERT: D 638 THR cc_start: 0.8811 (t) cc_final: 0.8492 (p) REVERT: D 642 ASN cc_start: 0.8681 (t0) cc_final: 0.8329 (t0) REVERT: D 699 LYS cc_start: 0.9200 (tptm) cc_final: 0.8722 (tppp) REVERT: D 717 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 723 GLU cc_start: 0.8378 (mp0) cc_final: 0.7973 (mt-10) REVERT: D 751 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 752 LYS cc_start: 0.8855 (tptp) cc_final: 0.8388 (tptp) REVERT: D 755 LYS cc_start: 0.8794 (tttt) cc_final: 0.8377 (tptp) REVERT: D 768 TYR cc_start: 0.7001 (m-10) cc_final: 0.6543 (m-10) REVERT: D 771 GLU cc_start: 0.8129 (pp20) cc_final: 0.7549 (pp20) REVERT: E 253 GLU cc_start: 0.8185 (pm20) cc_final: 0.7980 (mp0) REVERT: E 266 HIS cc_start: 0.8635 (m-70) cc_final: 0.8183 (m170) REVERT: E 292 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8459 (mtmm) REVERT: E 297 ARG cc_start: 0.8363 (tpt90) cc_final: 0.7941 (tpt90) REVERT: E 311 ASN cc_start: 0.7906 (m-40) cc_final: 0.7684 (t0) REVERT: E 382 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6725 (mtpt) REVERT: E 443 LYS cc_start: 0.8891 (tppt) cc_final: 0.8403 (tppt) REVERT: E 444 TYR cc_start: 0.8915 (t80) cc_final: 0.8398 (t80) REVERT: E 461 CYS cc_start: 0.8725 (m) cc_final: 0.8422 (t) REVERT: E 484 LEU cc_start: 0.8122 (mp) cc_final: 0.7868 (tp) REVERT: E 490 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8159 (t0) REVERT: E 512 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8036 (ttpt) REVERT: E 530 GLU cc_start: 0.8276 (tt0) cc_final: 0.7958 (tt0) REVERT: E 556 TYR cc_start: 0.8531 (p90) cc_final: 0.8040 (p90) REVERT: E 573 GLU cc_start: 0.8364 (pt0) cc_final: 0.7903 (tm-30) REVERT: E 619 ASP cc_start: 0.8341 (m-30) cc_final: 0.7975 (m-30) REVERT: E 642 ASN cc_start: 0.8557 (t0) cc_final: 0.8295 (t0) REVERT: E 651 LYS cc_start: 0.8592 (tppt) cc_final: 0.8330 (mmmm) REVERT: E 661 ARG cc_start: 0.6864 (tpt90) cc_final: 0.6406 (tpt170) REVERT: E 663 ASP cc_start: 0.8855 (p0) cc_final: 0.8377 (p0) REVERT: E 664 GLU cc_start: 0.8523 (tt0) cc_final: 0.8012 (tt0) REVERT: E 691 GLU cc_start: 0.8447 (tp30) cc_final: 0.8207 (tp30) REVERT: E 696 CYS cc_start: 0.8843 (t) cc_final: 0.8534 (t) REVERT: E 710 HIS cc_start: 0.8997 (m-70) cc_final: 0.8766 (m90) REVERT: E 715 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.7748 (ttp80) REVERT: E 723 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8149 (mm-30) REVERT: E 745 VAL cc_start: 0.8467 (t) cc_final: 0.7938 (m) REVERT: E 752 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8397 (tmtt) REVERT: E 771 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7802 (tm-30) REVERT: F 308 LEU cc_start: 0.8960 (mp) cc_final: 0.8699 (mp) REVERT: F 311 ASN cc_start: 0.8139 (t0) cc_final: 0.7736 (t0) REVERT: F 333 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7643 (tm-30) REVERT: F 335 ARG cc_start: 0.8707 (mtp85) cc_final: 0.8489 (mtp-110) REVERT: F 377 MET cc_start: 0.7946 (mpp) cc_final: 0.7594 (mpp) REVERT: F 393 ASN cc_start: 0.8850 (m-40) cc_final: 0.8638 (m-40) REVERT: F 444 TYR cc_start: 0.8948 (t80) cc_final: 0.8279 (t80) REVERT: F 468 THR cc_start: 0.8674 (m) cc_final: 0.8142 (p) REVERT: F 485 LYS cc_start: 0.8496 (mmtt) cc_final: 0.7851 (mmtt) REVERT: F 490 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7711 (t0) REVERT: F 513 VAL cc_start: 0.8744 (m) cc_final: 0.8302 (p) REVERT: F 536 LEU cc_start: 0.8940 (mm) cc_final: 0.8586 (tp) REVERT: F 540 GLU cc_start: 0.7852 (pp20) cc_final: 0.7465 (pp20) REVERT: F 572 THR cc_start: 0.8663 (m) cc_final: 0.8082 (p) REVERT: F 604 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8725 (ttmm) REVERT: F 642 ASN cc_start: 0.8491 (t0) cc_final: 0.8203 (t0) REVERT: F 661 ARG cc_start: 0.7118 (tpt170) cc_final: 0.6367 (tpt170) REVERT: F 663 ASP cc_start: 0.8444 (p0) cc_final: 0.8067 (p0) REVERT: F 687 ASN cc_start: 0.8821 (t0) cc_final: 0.8571 (t0) REVERT: F 691 GLU cc_start: 0.8521 (tp30) cc_final: 0.7925 (tp30) REVERT: F 699 LYS cc_start: 0.9117 (tptp) cc_final: 0.8698 (tppt) REVERT: F 723 GLU cc_start: 0.8395 (mp0) cc_final: 0.8182 (mt-10) REVERT: F 728 CYS cc_start: 0.8815 (m) cc_final: 0.8513 (m) REVERT: F 729 GLN cc_start: 0.8711 (mt0) cc_final: 0.8326 (mt0) REVERT: F 746 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7761 (mp0) REVERT: F 751 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7696 (tm-30) REVERT: F 754 PHE cc_start: 0.8734 (t80) cc_final: 0.8490 (t80) REVERT: F 775 ARG cc_start: 0.8221 (ttp80) cc_final: 0.8006 (ttp80) outliers start: 72 outliers final: 40 residues processed: 973 average time/residue: 0.1961 time to fit residues: 277.0418 Evaluate side-chains 958 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 906 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 529 LYS Chi-restraints excluded: chain F residue 618 ILE Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 196 optimal weight: 0.0170 chunk 101 optimal weight: 3.9990 chunk 290 optimal weight: 0.0870 chunk 297 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 301 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN F 426 GLN ** F 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.136402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114012 restraints weight = 43968.271| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.48 r_work: 0.3339 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25790 Z= 0.125 Angle : 0.649 10.128 34986 Z= 0.323 Chirality : 0.044 0.205 4020 Planarity : 0.005 0.077 4488 Dihedral : 12.485 156.865 3816 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.56 % Allowed : 18.07 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3240 helix: 0.99 (0.13), residues: 1566 sheet: 0.23 (0.29), residues: 366 loop : -0.31 (0.19), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 775 TYR 0.034 0.002 TYR C 444 PHE 0.035 0.002 PHE D 587 TRP 0.008 0.002 TRP F 515 HIS 0.015 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00280 (25782) covalent geometry : angle 0.64944 (34986) hydrogen bonds : bond 0.03819 ( 1230) hydrogen bonds : angle 4.29289 ( 3498) Misc. bond : bond 0.00121 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 940 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8812 (tp) REVERT: A 297 ARG cc_start: 0.8687 (tpt170) cc_final: 0.8302 (tpt170) REVERT: A 335 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8370 (mtp-110) REVERT: A 408 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 429 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8190 (mmm-85) REVERT: A 443 LYS cc_start: 0.8952 (mmpt) cc_final: 0.8627 (tppt) REVERT: A 444 TYR cc_start: 0.8731 (t80) cc_final: 0.8423 (t80) REVERT: A 488 LEU cc_start: 0.8068 (tp) cc_final: 0.7721 (tt) REVERT: A 492 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: A 512 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8313 (tttm) REVERT: A 514 TYR cc_start: 0.8699 (m-10) cc_final: 0.8255 (m-10) REVERT: A 523 GLU cc_start: 0.8193 (tp30) cc_final: 0.7423 (tp30) REVERT: A 525 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8727 (ttmt) REVERT: A 530 GLU cc_start: 0.8081 (tt0) cc_final: 0.7660 (tt0) REVERT: A 540 GLU cc_start: 0.7916 (pp20) cc_final: 0.7511 (pp20) REVERT: A 548 SER cc_start: 0.8989 (m) cc_final: 0.8386 (p) REVERT: A 556 TYR cc_start: 0.8451 (p90) cc_final: 0.8109 (p90) REVERT: A 572 THR cc_start: 0.8630 (m) cc_final: 0.8427 (p) REVERT: A 586 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 595 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 651 LYS cc_start: 0.8971 (tppt) cc_final: 0.8690 (tptp) REVERT: A 663 ASP cc_start: 0.7975 (p0) cc_final: 0.7562 (p0) REVERT: A 695 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8527 (tptp) REVERT: A 717 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8020 (tm-30) REVERT: A 730 GLU cc_start: 0.8447 (tp30) cc_final: 0.8108 (tp30) REVERT: A 737 MET cc_start: 0.7332 (ttm) cc_final: 0.7115 (ttm) REVERT: A 751 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 752 LYS cc_start: 0.8943 (tttm) cc_final: 0.8536 (ttmm) REVERT: A 755 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8564 (ttmt) REVERT: A 764 GLU cc_start: 0.7889 (mp0) cc_final: 0.7636 (mp0) REVERT: A 770 GLU cc_start: 0.7963 (mp0) cc_final: 0.7760 (mp0) REVERT: B 301 ASN cc_start: 0.8817 (t0) cc_final: 0.8477 (t0) REVERT: B 311 ASN cc_start: 0.8074 (t0) cc_final: 0.7833 (t0) REVERT: B 324 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: B 328 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8277 (ttm110) REVERT: B 333 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7614 (tm-30) REVERT: B 406 ASP cc_start: 0.7621 (t0) cc_final: 0.7121 (t0) REVERT: B 421 ASP cc_start: 0.8793 (t0) cc_final: 0.8362 (t0) REVERT: B 430 MET cc_start: 0.8528 (ptt) cc_final: 0.8326 (ptt) REVERT: B 463 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8129 (mm-30) REVERT: B 468 THR cc_start: 0.8698 (m) cc_final: 0.8125 (p) REVERT: B 486 VAL cc_start: 0.9028 (p) cc_final: 0.8805 (m) REVERT: B 490 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 493 SER cc_start: 0.8977 (t) cc_final: 0.8584 (p) REVERT: B 497 ASP cc_start: 0.8098 (t0) cc_final: 0.7602 (t0) REVERT: B 512 LYS cc_start: 0.8377 (ttpp) cc_final: 0.7998 (ttpp) REVERT: B 525 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8364 (mmtp) REVERT: B 534 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8579 (tp) REVERT: B 540 GLU cc_start: 0.8078 (pp20) cc_final: 0.7738 (pp20) REVERT: B 548 SER cc_start: 0.8832 (t) cc_final: 0.8462 (p) REVERT: B 556 TYR cc_start: 0.8534 (p90) cc_final: 0.8192 (p90) REVERT: B 582 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8381 (mtmm) REVERT: B 585 GLU cc_start: 0.8228 (pt0) cc_final: 0.7542 (pp20) REVERT: B 587 PHE cc_start: 0.7991 (t80) cc_final: 0.7545 (t80) REVERT: B 600 GLU cc_start: 0.8118 (pp20) cc_final: 0.7592 (pp20) REVERT: B 617 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7765 (mm-30) REVERT: B 637 LEU cc_start: 0.9087 (tt) cc_final: 0.8884 (tt) REVERT: B 638 THR cc_start: 0.8648 (t) cc_final: 0.8387 (p) REVERT: B 641 LEU cc_start: 0.9087 (mt) cc_final: 0.8848 (mm) REVERT: B 642 ASN cc_start: 0.8741 (t0) cc_final: 0.8431 (t0) REVERT: B 643 GLU cc_start: 0.8732 (tp30) cc_final: 0.8262 (tp30) REVERT: B 663 ASP cc_start: 0.8244 (p0) cc_final: 0.7885 (p0) REVERT: B 676 ASP cc_start: 0.8500 (p0) cc_final: 0.7754 (p0) REVERT: B 678 HIS cc_start: 0.8032 (m170) cc_final: 0.7543 (m170) REVERT: B 694 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8279 (mtpt) REVERT: B 695 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8375 (tptm) REVERT: B 696 CYS cc_start: 0.8848 (t) cc_final: 0.8514 (t) REVERT: B 751 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7608 (tp30) REVERT: B 755 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8424 (ttmm) REVERT: B 770 GLU cc_start: 0.8517 (tp30) cc_final: 0.8230 (mm-30) REVERT: B 771 GLU cc_start: 0.8084 (pp20) cc_final: 0.7775 (pp20) REVERT: C 253 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: C 255 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 262 GLU cc_start: 0.8447 (tp30) cc_final: 0.8060 (tm-30) REVERT: C 267 GLN cc_start: 0.8890 (pt0) cc_final: 0.8531 (pt0) REVERT: C 292 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8495 (mttp) REVERT: C 324 GLU cc_start: 0.7417 (mp0) cc_final: 0.6700 (mp0) REVERT: C 333 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7496 (tp30) REVERT: C 382 LYS cc_start: 0.7411 (mtmt) cc_final: 0.7112 (mtmm) REVERT: C 393 ASN cc_start: 0.8714 (m-40) cc_final: 0.8475 (m-40) REVERT: C 406 ASP cc_start: 0.7344 (t0) cc_final: 0.6644 (m-30) REVERT: C 410 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7831 (mm-30) REVERT: C 421 ASP cc_start: 0.8553 (t0) cc_final: 0.8179 (t0) REVERT: C 426 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8382 (mm-40) REVERT: C 484 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8116 (mm) REVERT: C 488 LEU cc_start: 0.7674 (tp) cc_final: 0.7200 (tt) REVERT: C 490 ASP cc_start: 0.8543 (t0) cc_final: 0.7722 (t0) REVERT: C 492 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: C 493 SER cc_start: 0.8860 (t) cc_final: 0.8516 (p) REVERT: C 495 MET cc_start: 0.8769 (ttp) cc_final: 0.8540 (ttm) REVERT: C 497 ASP cc_start: 0.8058 (t0) cc_final: 0.7802 (t0) REVERT: C 512 LYS cc_start: 0.8593 (mmmt) cc_final: 0.7975 (mmmt) REVERT: C 522 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7978 (mm-30) REVERT: C 525 LYS cc_start: 0.8610 (tppp) cc_final: 0.8323 (tppp) REVERT: C 577 ASN cc_start: 0.8584 (t0) cc_final: 0.8329 (t0) REVERT: C 582 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8364 (mmmm) REVERT: C 595 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7995 (mt-10) REVERT: C 599 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.8308 (mtt-85) REVERT: C 664 GLU cc_start: 0.8465 (tt0) cc_final: 0.8248 (tt0) REVERT: C 666 ASP cc_start: 0.8319 (t0) cc_final: 0.7771 (p0) REVERT: C 691 GLU cc_start: 0.8471 (tp30) cc_final: 0.7864 (tp30) REVERT: C 730 GLU cc_start: 0.8579 (tp30) cc_final: 0.8080 (mm-30) REVERT: C 739 ASP cc_start: 0.7629 (t0) cc_final: 0.7375 (t0) REVERT: C 751 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 755 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8207 (tmtt) REVERT: C 761 ILE cc_start: 0.8680 (tt) cc_final: 0.8403 (pt) REVERT: C 771 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7323 (pp20) REVERT: D 252 LYS cc_start: 0.8642 (tppp) cc_final: 0.8240 (tppp) REVERT: D 280 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7552 (mmm-85) REVERT: D 301 ASN cc_start: 0.8367 (m110) cc_final: 0.7913 (m110) REVERT: D 328 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8605 (ttm110) REVERT: D 333 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7170 (tm-30) REVERT: D 374 MET cc_start: 0.8320 (tpt) cc_final: 0.7826 (tpp) REVERT: D 423 LEU cc_start: 0.9215 (mt) cc_final: 0.8988 (mt) REVERT: D 426 GLN cc_start: 0.8836 (tp40) cc_final: 0.8370 (tp40) REVERT: D 443 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8392 (mmtp) REVERT: D 444 TYR cc_start: 0.8707 (t80) cc_final: 0.8244 (t80) REVERT: D 448 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8092 (ttmm) REVERT: D 453 VAL cc_start: 0.8905 (p) cc_final: 0.8535 (m) REVERT: D 461 CYS cc_start: 0.8655 (m) cc_final: 0.8177 (t) REVERT: D 463 GLU cc_start: 0.8603 (tp30) cc_final: 0.8303 (tp30) REVERT: D 488 LEU cc_start: 0.8122 (tp) cc_final: 0.7838 (tt) REVERT: D 492 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: D 497 ASP cc_start: 0.8364 (t0) cc_final: 0.8108 (t0) REVERT: D 512 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8141 (ttmm) REVERT: D 513 VAL cc_start: 0.8415 (m) cc_final: 0.8209 (p) REVERT: D 517 ASP cc_start: 0.8679 (m-30) cc_final: 0.8456 (m-30) REVERT: D 523 GLU cc_start: 0.8027 (tp30) cc_final: 0.7003 (tp30) REVERT: D 525 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8659 (mmmm) REVERT: D 527 LYS cc_start: 0.8857 (mtpp) cc_final: 0.7992 (ttmm) REVERT: D 537 GLU cc_start: 0.8079 (mp0) cc_final: 0.7590 (mp0) REVERT: D 563 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8327 (mtmt) REVERT: D 600 GLU cc_start: 0.8076 (pp20) cc_final: 0.7684 (pp20) REVERT: D 604 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8490 (ttmt) REVERT: D 638 THR cc_start: 0.8765 (t) cc_final: 0.8431 (p) REVERT: D 642 ASN cc_start: 0.8717 (t0) cc_final: 0.8328 (t0) REVERT: D 661 ARG cc_start: 0.6987 (tpt170) cc_final: 0.6640 (tpt170) REVERT: D 699 LYS cc_start: 0.9177 (tptm) cc_final: 0.8734 (tppp) REVERT: D 717 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7991 (tm-30) REVERT: D 737 MET cc_start: 0.7537 (ttm) cc_final: 0.7316 (ttm) REVERT: D 751 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7638 (tm-30) REVERT: D 755 LYS cc_start: 0.8771 (tttt) cc_final: 0.8357 (tptp) REVERT: D 775 ARG cc_start: 0.7154 (ttp80) cc_final: 0.6722 (ttp80) REVERT: E 262 GLU cc_start: 0.8500 (tp30) cc_final: 0.8219 (tp30) REVERT: E 297 ARG cc_start: 0.8527 (tpt90) cc_final: 0.8039 (tpt90) REVERT: E 311 ASN cc_start: 0.7886 (m-40) cc_final: 0.7678 (t0) REVERT: E 382 LYS cc_start: 0.7226 (mtpt) cc_final: 0.7009 (mmmt) REVERT: E 430 MET cc_start: 0.8235 (ptt) cc_final: 0.7969 (ptt) REVERT: E 443 LYS cc_start: 0.8926 (tppt) cc_final: 0.8504 (tppt) REVERT: E 444 TYR cc_start: 0.8875 (t80) cc_final: 0.8486 (t80) REVERT: E 461 CYS cc_start: 0.8763 (m) cc_final: 0.8444 (t) REVERT: E 468 THR cc_start: 0.8608 (m) cc_final: 0.7998 (p) REVERT: E 490 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8007 (t0) REVERT: E 512 LYS cc_start: 0.8389 (ttpt) cc_final: 0.7749 (ttpt) REVERT: E 556 TYR cc_start: 0.8447 (p90) cc_final: 0.8076 (p90) REVERT: E 573 GLU cc_start: 0.8337 (pt0) cc_final: 0.8042 (tm-30) REVERT: E 642 ASN cc_start: 0.8566 (t0) cc_final: 0.8332 (t0) REVERT: E 660 ASN cc_start: 0.8753 (p0) cc_final: 0.8549 (p0) REVERT: E 661 ARG cc_start: 0.6559 (tpt90) cc_final: 0.6154 (tpt170) REVERT: E 663 ASP cc_start: 0.8688 (p0) cc_final: 0.8386 (p0) REVERT: E 691 GLU cc_start: 0.8379 (tp30) cc_final: 0.7951 (tp30) REVERT: E 696 CYS cc_start: 0.8811 (t) cc_final: 0.8516 (t) REVERT: E 704 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 715 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.7828 (ttp80) REVERT: E 745 VAL cc_start: 0.8463 (t) cc_final: 0.7962 (m) REVERT: E 752 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8511 (ttmm) REVERT: E 755 LYS cc_start: 0.8785 (tptm) cc_final: 0.8365 (tptm) REVERT: E 770 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8310 (mm-30) REVERT: E 771 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7822 (tm-30) REVERT: F 262 GLU cc_start: 0.8488 (tp30) cc_final: 0.8286 (tp30) REVERT: F 280 ARG cc_start: 0.7854 (mtt90) cc_final: 0.7563 (mtt180) REVERT: F 311 ASN cc_start: 0.8002 (t0) cc_final: 0.7645 (t0) REVERT: F 335 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8395 (mtp-110) REVERT: F 391 ARG cc_start: 0.8027 (mtm180) cc_final: 0.7817 (mtm-85) REVERT: F 401 ARG cc_start: 0.7769 (mmp80) cc_final: 0.7541 (tpp80) REVERT: F 426 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8436 (mm-40) REVERT: F 443 LYS cc_start: 0.8685 (mmpt) cc_final: 0.8442 (mmpt) REVERT: F 444 TYR cc_start: 0.8925 (t80) cc_final: 0.8218 (t80) REVERT: F 468 THR cc_start: 0.8646 (m) cc_final: 0.8203 (p) REVERT: F 485 LYS cc_start: 0.8508 (mmtt) cc_final: 0.7949 (mmtt) REVERT: F 488 LEU cc_start: 0.7702 (tp) cc_final: 0.7394 (tt) REVERT: F 490 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7810 (t0) REVERT: F 512 LYS cc_start: 0.8311 (tppp) cc_final: 0.8004 (tppp) REVERT: F 513 VAL cc_start: 0.8746 (m) cc_final: 0.8440 (p) REVERT: F 522 GLU cc_start: 0.8176 (tp30) cc_final: 0.7890 (mp0) REVERT: F 536 LEU cc_start: 0.8942 (mm) cc_final: 0.8610 (tp) REVERT: F 540 GLU cc_start: 0.7835 (pp20) cc_final: 0.7434 (pp20) REVERT: F 572 THR cc_start: 0.8734 (m) cc_final: 0.8285 (p) REVERT: F 642 ASN cc_start: 0.8407 (t0) cc_final: 0.8126 (t0) REVERT: F 661 ARG cc_start: 0.7060 (tpt170) cc_final: 0.6473 (tpt170) REVERT: F 663 ASP cc_start: 0.8470 (p0) cc_final: 0.8242 (p0) REVERT: F 687 ASN cc_start: 0.8799 (t0) cc_final: 0.8555 (t0) REVERT: F 697 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8695 (t) REVERT: F 723 GLU cc_start: 0.8414 (mp0) cc_final: 0.8111 (mt-10) REVERT: F 729 GLN cc_start: 0.8617 (mt0) cc_final: 0.8294 (mt0) REVERT: F 746 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7707 (mp0) REVERT: F 751 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7605 (tm-30) REVERT: F 754 PHE cc_start: 0.8627 (t80) cc_final: 0.8371 (t80) REVERT: F 755 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8384 (ttmm) outliers start: 96 outliers final: 51 residues processed: 972 average time/residue: 0.1964 time to fit residues: 278.1550 Evaluate side-chains 973 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 906 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 443 LYS Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 645 ASP Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 762 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 618 ILE Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110905 restraints weight = 44473.941| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.46 r_work: 0.3278 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 25790 Z= 0.223 Angle : 0.686 9.402 34986 Z= 0.347 Chirality : 0.046 0.187 4020 Planarity : 0.005 0.091 4488 Dihedral : 12.617 173.271 3816 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.93 % Allowed : 19.44 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3240 helix: 1.03 (0.13), residues: 1590 sheet: 0.46 (0.30), residues: 348 loop : -0.25 (0.19), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 775 TYR 0.049 0.002 TYR C 444 PHE 0.035 0.002 PHE D 587 TRP 0.009 0.002 TRP E 515 HIS 0.009 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00488 (25782) covalent geometry : angle 0.68644 (34986) hydrogen bonds : bond 0.04096 ( 1230) hydrogen bonds : angle 4.31578 ( 3498) Misc. bond : bond 0.00073 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 954 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8355 (m-30) cc_final: 0.7991 (m-30) REVERT: A 253 GLU cc_start: 0.8389 (pm20) cc_final: 0.8070 (pm20) REVERT: A 262 GLU cc_start: 0.8559 (tp30) cc_final: 0.8036 (tm-30) REVERT: A 297 ARG cc_start: 0.8801 (tpt170) cc_final: 0.8461 (tpt170) REVERT: A 301 ASN cc_start: 0.8845 (t0) cc_final: 0.8623 (t0) REVERT: A 333 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7486 (tm-30) REVERT: A 335 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8390 (mtp-110) REVERT: A 426 GLN cc_start: 0.8901 (tp40) cc_final: 0.8669 (mm-40) REVERT: A 429 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8300 (mmm-85) REVERT: A 443 LYS cc_start: 0.9066 (mmpt) cc_final: 0.8676 (tppt) REVERT: A 444 TYR cc_start: 0.8768 (t80) cc_final: 0.8453 (t80) REVERT: A 488 LEU cc_start: 0.8228 (tp) cc_final: 0.7885 (tp) REVERT: A 492 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: A 512 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8445 (ttpp) REVERT: A 514 TYR cc_start: 0.8809 (m-10) cc_final: 0.8451 (m-10) REVERT: A 522 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 523 GLU cc_start: 0.8267 (tp30) cc_final: 0.7543 (tp30) REVERT: A 540 GLU cc_start: 0.7991 (pp20) cc_final: 0.7560 (pp20) REVERT: A 548 SER cc_start: 0.8926 (m) cc_final: 0.8314 (p) REVERT: A 556 TYR cc_start: 0.8520 (p90) cc_final: 0.8163 (p90) REVERT: A 586 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8568 (tp) REVERT: A 595 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8353 (mt-10) REVERT: A 651 LYS cc_start: 0.9004 (tppt) cc_final: 0.8712 (tppt) REVERT: A 661 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7138 (mmm160) REVERT: A 663 ASP cc_start: 0.7952 (p0) cc_final: 0.6952 (p0) REVERT: A 691 GLU cc_start: 0.8657 (tp30) cc_final: 0.8015 (tp30) REVERT: A 695 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8584 (tptp) REVERT: A 717 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 730 GLU cc_start: 0.8436 (tp30) cc_final: 0.7995 (mm-30) REVERT: A 737 MET cc_start: 0.7512 (ttm) cc_final: 0.7299 (ttm) REVERT: A 751 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 752 LYS cc_start: 0.8983 (tttm) cc_final: 0.8552 (ttmm) REVERT: A 755 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8566 (ttmt) REVERT: A 764 GLU cc_start: 0.7940 (mp0) cc_final: 0.7587 (mp0) REVERT: B 253 GLU cc_start: 0.8402 (mp0) cc_final: 0.8036 (mp0) REVERT: B 262 GLU cc_start: 0.8519 (tp30) cc_final: 0.8191 (tm-30) REVERT: B 297 ARG cc_start: 0.8815 (tpt170) cc_final: 0.8497 (tpt170) REVERT: B 301 ASN cc_start: 0.8850 (t0) cc_final: 0.8526 (t0) REVERT: B 311 ASN cc_start: 0.8121 (t0) cc_final: 0.7869 (t0) REVERT: B 324 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: B 328 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8303 (ttm110) REVERT: B 333 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 382 LYS cc_start: 0.7301 (mtmt) cc_final: 0.7013 (mtpt) REVERT: B 391 ARG cc_start: 0.8283 (ptt-90) cc_final: 0.7564 (ptt-90) REVERT: B 421 ASP cc_start: 0.8795 (t0) cc_final: 0.8370 (t0) REVERT: B 430 MET cc_start: 0.8736 (ptt) cc_final: 0.8516 (ptt) REVERT: B 448 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8375 (mtpt) REVERT: B 463 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 468 THR cc_start: 0.8749 (m) cc_final: 0.8209 (p) REVERT: B 486 VAL cc_start: 0.9006 (p) cc_final: 0.8772 (m) REVERT: B 490 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7876 (t0) REVERT: B 492 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: B 493 SER cc_start: 0.8932 (t) cc_final: 0.8607 (p) REVERT: B 512 LYS cc_start: 0.8330 (ttpp) cc_final: 0.7915 (ttpp) REVERT: B 525 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8479 (mmtp) REVERT: B 534 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8696 (tp) REVERT: B 540 GLU cc_start: 0.8121 (pp20) cc_final: 0.7794 (pp20) REVERT: B 582 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8457 (mtmm) REVERT: B 585 GLU cc_start: 0.8314 (pt0) cc_final: 0.7545 (pp20) REVERT: B 587 PHE cc_start: 0.8010 (t80) cc_final: 0.7574 (t80) REVERT: B 600 GLU cc_start: 0.8353 (pp20) cc_final: 0.7822 (pp20) REVERT: B 617 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7926 (mm-30) REVERT: B 638 THR cc_start: 0.8740 (t) cc_final: 0.8438 (p) REVERT: B 642 ASN cc_start: 0.8787 (t0) cc_final: 0.8480 (t0) REVERT: B 643 GLU cc_start: 0.8727 (tp30) cc_final: 0.8270 (tp30) REVERT: B 660 ASN cc_start: 0.8576 (p0) cc_final: 0.7428 (p0) REVERT: B 663 ASP cc_start: 0.8276 (p0) cc_final: 0.7905 (p0) REVERT: B 676 ASP cc_start: 0.8528 (p0) cc_final: 0.8120 (p0) REVERT: B 678 HIS cc_start: 0.8145 (m170) cc_final: 0.7733 (m170) REVERT: B 694 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8344 (mtpt) REVERT: B 695 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8450 (tptm) REVERT: B 696 CYS cc_start: 0.8876 (t) cc_final: 0.8536 (t) REVERT: B 711 GLU cc_start: 0.7840 (pp20) cc_final: 0.7609 (pp20) REVERT: B 751 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7726 (tp30) REVERT: B 755 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8512 (ttmm) REVERT: B 765 MET cc_start: 0.8361 (mtp) cc_final: 0.8112 (mtp) REVERT: B 770 GLU cc_start: 0.8599 (tp30) cc_final: 0.8278 (mm-30) REVERT: B 775 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7407 (ttp80) REVERT: C 255 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 262 GLU cc_start: 0.8487 (tp30) cc_final: 0.8076 (tm-30) REVERT: C 267 GLN cc_start: 0.9009 (pt0) cc_final: 0.8565 (pt0) REVERT: C 333 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7517 (tp30) REVERT: C 382 LYS cc_start: 0.7446 (mtmt) cc_final: 0.7184 (mtmm) REVERT: C 393 ASN cc_start: 0.8778 (m-40) cc_final: 0.8555 (m-40) REVERT: C 406 ASP cc_start: 0.7664 (t0) cc_final: 0.6902 (m-30) REVERT: C 421 ASP cc_start: 0.8600 (t0) cc_final: 0.8109 (t0) REVERT: C 425 LYS cc_start: 0.8990 (mttp) cc_final: 0.8721 (mttp) REVERT: C 426 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8485 (mm-40) REVERT: C 484 LEU cc_start: 0.8545 (mm) cc_final: 0.8190 (mm) REVERT: C 488 LEU cc_start: 0.7940 (tp) cc_final: 0.7370 (tt) REVERT: C 490 ASP cc_start: 0.8543 (t0) cc_final: 0.7755 (t0) REVERT: C 492 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: C 493 SER cc_start: 0.8944 (t) cc_final: 0.8632 (p) REVERT: C 495 MET cc_start: 0.8825 (ttp) cc_final: 0.8591 (ttm) REVERT: C 497 ASP cc_start: 0.8125 (t0) cc_final: 0.7887 (t0) REVERT: C 512 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8108 (mmmt) REVERT: C 522 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8029 (mm-30) REVERT: C 525 LYS cc_start: 0.8652 (tppp) cc_final: 0.8270 (tppp) REVERT: C 582 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8501 (mmmm) REVERT: C 595 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8033 (mt-10) REVERT: C 599 ARG cc_start: 0.8763 (mtt-85) cc_final: 0.8356 (mtt-85) REVERT: C 600 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: C 691 GLU cc_start: 0.8521 (tp30) cc_final: 0.7921 (tp30) REVERT: C 696 CYS cc_start: 0.8527 (t) cc_final: 0.8041 (p) REVERT: C 699 LYS cc_start: 0.9113 (tptp) cc_final: 0.8797 (tppt) REVERT: C 710 HIS cc_start: 0.8864 (m90) cc_final: 0.8589 (m-70) REVERT: C 730 GLU cc_start: 0.8571 (tp30) cc_final: 0.8073 (mm-30) REVERT: C 739 ASP cc_start: 0.7691 (t0) cc_final: 0.7409 (t0) REVERT: C 751 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 755 LYS cc_start: 0.8646 (tmtt) cc_final: 0.8292 (tmtt) REVERT: C 771 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7575 (pp20) REVERT: D 252 LYS cc_start: 0.8680 (tppp) cc_final: 0.8312 (tppp) REVERT: D 262 GLU cc_start: 0.8455 (tp30) cc_final: 0.8237 (tm-30) REVERT: D 328 ARG cc_start: 0.8927 (ttm110) cc_final: 0.8623 (ttm110) REVERT: D 333 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 374 MET cc_start: 0.8398 (tpt) cc_final: 0.7950 (tpp) REVERT: D 425 LYS cc_start: 0.8964 (mttm) cc_final: 0.8676 (ttmm) REVERT: D 426 GLN cc_start: 0.8947 (tp40) cc_final: 0.8540 (tp40) REVERT: D 443 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8461 (mmtp) REVERT: D 444 TYR cc_start: 0.8789 (t80) cc_final: 0.8279 (t80) REVERT: D 448 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8047 (ttmm) REVERT: D 461 CYS cc_start: 0.8686 (m) cc_final: 0.8293 (t) REVERT: D 463 GLU cc_start: 0.8700 (tp30) cc_final: 0.8323 (mm-30) REVERT: D 488 LEU cc_start: 0.8215 (tp) cc_final: 0.7848 (tt) REVERT: D 492 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: D 497 ASP cc_start: 0.8480 (t0) cc_final: 0.8231 (t0) REVERT: D 512 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8074 (ttmm) REVERT: D 513 VAL cc_start: 0.8558 (m) cc_final: 0.8249 (p) REVERT: D 523 GLU cc_start: 0.8140 (tp30) cc_final: 0.7132 (tp30) REVERT: D 525 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8651 (mmmm) REVERT: D 527 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8192 (ttmm) REVERT: D 600 GLU cc_start: 0.8239 (pp20) cc_final: 0.7830 (pp20) REVERT: D 604 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8565 (ttmt) REVERT: D 642 ASN cc_start: 0.8719 (t0) cc_final: 0.8347 (t0) REVERT: D 661 ARG cc_start: 0.7039 (tpt170) cc_final: 0.6681 (tpt170) REVERT: D 699 LYS cc_start: 0.9181 (tptm) cc_final: 0.8726 (tppp) REVERT: D 717 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8185 (tm-30) REVERT: D 737 MET cc_start: 0.7732 (ttm) cc_final: 0.7516 (ttm) REVERT: D 751 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 755 LYS cc_start: 0.8855 (tttt) cc_final: 0.8444 (tptp) REVERT: D 768 TYR cc_start: 0.7046 (m-10) cc_final: 0.6722 (m-10) REVERT: D 771 GLU cc_start: 0.8097 (pp20) cc_final: 0.7704 (pp20) REVERT: E 255 GLU cc_start: 0.8918 (tt0) cc_final: 0.8712 (tt0) REVERT: E 262 GLU cc_start: 0.8541 (tp30) cc_final: 0.8017 (tm-30) REVERT: E 297 ARG cc_start: 0.8668 (tpt90) cc_final: 0.8205 (tpt90) REVERT: E 311 ASN cc_start: 0.7931 (m-40) cc_final: 0.7708 (t0) REVERT: E 382 LYS cc_start: 0.7424 (mtpt) cc_final: 0.7197 (mmmt) REVERT: E 401 ARG cc_start: 0.8134 (mmp80) cc_final: 0.7644 (tpp80) REVERT: E 426 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8736 (mm-40) REVERT: E 430 MET cc_start: 0.8589 (ptt) cc_final: 0.8366 (ptt) REVERT: E 443 LYS cc_start: 0.8979 (tppt) cc_final: 0.8557 (tppt) REVERT: E 444 TYR cc_start: 0.8913 (t80) cc_final: 0.8472 (t80) REVERT: E 461 CYS cc_start: 0.8770 (m) cc_final: 0.8394 (t) REVERT: E 490 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8071 (t0) REVERT: E 512 LYS cc_start: 0.8473 (ttpt) cc_final: 0.7956 (ttpt) REVERT: E 530 GLU cc_start: 0.8231 (tt0) cc_final: 0.7818 (tt0) REVERT: E 600 GLU cc_start: 0.8343 (pp20) cc_final: 0.7877 (pp20) REVERT: E 619 ASP cc_start: 0.8504 (m-30) cc_final: 0.8118 (m-30) REVERT: E 642 ASN cc_start: 0.8632 (t0) cc_final: 0.8387 (t0) REVERT: E 661 ARG cc_start: 0.6784 (tpt90) cc_final: 0.6158 (tpt90) REVERT: E 663 ASP cc_start: 0.8709 (p0) cc_final: 0.8243 (p0) REVERT: E 664 GLU cc_start: 0.8595 (tt0) cc_final: 0.8342 (tt0) REVERT: E 678 HIS cc_start: 0.8208 (m170) cc_final: 0.7840 (m170) REVERT: E 691 GLU cc_start: 0.8421 (tp30) cc_final: 0.8178 (tp30) REVERT: E 696 CYS cc_start: 0.8788 (t) cc_final: 0.8471 (t) REVERT: E 715 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.7875 (ttp80) REVERT: E 717 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8214 (tm-30) REVERT: E 745 VAL cc_start: 0.8560 (t) cc_final: 0.8078 (m) REVERT: E 752 LYS cc_start: 0.8887 (tmtt) cc_final: 0.8526 (ttmm) REVERT: E 755 LYS cc_start: 0.8876 (tptm) cc_final: 0.8501 (tptm) REVERT: E 770 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8340 (mm-30) REVERT: E 771 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7849 (tm-30) REVERT: F 253 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: F 262 GLU cc_start: 0.8528 (tp30) cc_final: 0.8181 (tm-30) REVERT: F 280 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7634 (mtt180) REVERT: F 311 ASN cc_start: 0.8081 (t0) cc_final: 0.7692 (t0) REVERT: F 333 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7678 (tp30) REVERT: F 335 ARG cc_start: 0.8757 (mtp85) cc_final: 0.8519 (mtp-110) REVERT: F 391 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7750 (mtm-85) REVERT: F 406 ASP cc_start: 0.7028 (t0) cc_final: 0.6341 (m-30) REVERT: F 443 LYS cc_start: 0.8795 (mmpt) cc_final: 0.8452 (tppt) REVERT: F 444 TYR cc_start: 0.8969 (t80) cc_final: 0.8200 (t80) REVERT: F 463 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8557 (mm-30) REVERT: F 468 THR cc_start: 0.8729 (m) cc_final: 0.8224 (p) REVERT: F 488 LEU cc_start: 0.7749 (tp) cc_final: 0.7420 (tt) REVERT: F 490 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.7947 (t0) REVERT: F 513 VAL cc_start: 0.8860 (m) cc_final: 0.8492 (p) REVERT: F 522 GLU cc_start: 0.8296 (tp30) cc_final: 0.7881 (mp0) REVERT: F 536 LEU cc_start: 0.9036 (mm) cc_final: 0.8688 (tp) REVERT: F 540 GLU cc_start: 0.7899 (pp20) cc_final: 0.7547 (pp20) REVERT: F 572 THR cc_start: 0.8809 (m) cc_final: 0.8385 (p) REVERT: F 642 ASN cc_start: 0.8453 (t0) cc_final: 0.8149 (t0) REVERT: F 661 ARG cc_start: 0.7279 (tpt170) cc_final: 0.6973 (tpt170) REVERT: F 676 ASP cc_start: 0.8242 (p0) cc_final: 0.7748 (p0) REVERT: F 687 ASN cc_start: 0.8854 (t0) cc_final: 0.8621 (t0) REVERT: F 691 GLU cc_start: 0.8537 (tp30) cc_final: 0.7792 (tp30) REVERT: F 697 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8679 (t) REVERT: F 699 LYS cc_start: 0.9139 (tptp) cc_final: 0.8873 (tppt) REVERT: F 723 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: F 729 GLN cc_start: 0.8658 (mt0) cc_final: 0.8292 (mt0) REVERT: F 746 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7742 (mp0) REVERT: F 751 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7635 (tm-30) REVERT: F 754 PHE cc_start: 0.8712 (t80) cc_final: 0.8446 (t80) REVERT: F 755 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8385 (ttmm) REVERT: F 771 GLU cc_start: 0.8106 (pp20) cc_final: 0.7637 (pp20) REVERT: F 775 ARG cc_start: 0.8268 (ttp80) cc_final: 0.8058 (ttp80) outliers start: 106 outliers final: 63 residues processed: 995 average time/residue: 0.1996 time to fit residues: 287.8469 Evaluate side-chains 989 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 911 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 582 LYS Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 486 VAL Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 529 LYS Chi-restraints excluded: chain F residue 618 ILE Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 723 GLU Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 119 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 11 optimal weight: 0.0020 chunk 262 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 ASN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112403 restraints weight = 44357.492| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.50 r_work: 0.3322 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25790 Z= 0.138 Angle : 0.665 13.441 34986 Z= 0.328 Chirality : 0.044 0.174 4020 Planarity : 0.005 0.083 4488 Dihedral : 12.414 179.301 3816 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.96 % Allowed : 21.07 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3240 helix: 1.10 (0.13), residues: 1590 sheet: 0.44 (0.29), residues: 348 loop : -0.19 (0.19), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 775 TYR 0.021 0.001 TYR C 444 PHE 0.033 0.002 PHE E 507 TRP 0.010 0.002 TRP A 515 HIS 0.006 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00317 (25782) covalent geometry : angle 0.66499 (34986) hydrogen bonds : bond 0.03723 ( 1230) hydrogen bonds : angle 4.17913 ( 3498) Misc. bond : bond 0.00079 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 912 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8272 (pm20) cc_final: 0.7925 (pm20) REVERT: A 262 GLU cc_start: 0.8456 (tp30) cc_final: 0.7953 (tm-30) REVERT: A 297 ARG cc_start: 0.8724 (tpt170) cc_final: 0.8401 (tpt170) REVERT: A 301 ASN cc_start: 0.8803 (t0) cc_final: 0.8577 (t0) REVERT: A 333 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 335 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8356 (mtp-110) REVERT: A 410 GLU cc_start: 0.8240 (tp30) cc_final: 0.7619 (mm-30) REVERT: A 426 GLN cc_start: 0.8876 (tp40) cc_final: 0.8636 (mm-40) REVERT: A 429 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8286 (mmm-85) REVERT: A 443 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8625 (tppt) REVERT: A 444 TYR cc_start: 0.8669 (t80) cc_final: 0.8300 (t80) REVERT: A 448 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8235 (mttt) REVERT: A 463 GLU cc_start: 0.8637 (tp30) cc_final: 0.8095 (tp30) REVERT: A 488 LEU cc_start: 0.8102 (tp) cc_final: 0.7744 (tp) REVERT: A 490 ASP cc_start: 0.8259 (t0) cc_final: 0.7745 (t0) REVERT: A 492 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: A 512 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8243 (tttm) REVERT: A 514 TYR cc_start: 0.8675 (m-10) cc_final: 0.8092 (m-10) REVERT: A 523 GLU cc_start: 0.8311 (tp30) cc_final: 0.7551 (tp30) REVERT: A 525 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8593 (ttmt) REVERT: A 540 GLU cc_start: 0.7971 (pp20) cc_final: 0.7545 (pp20) REVERT: A 548 SER cc_start: 0.8910 (m) cc_final: 0.8341 (p) REVERT: A 551 LYS cc_start: 0.8806 (tptt) cc_final: 0.8493 (tppp) REVERT: A 556 TYR cc_start: 0.8452 (p90) cc_final: 0.8080 (p90) REVERT: A 586 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 595 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8359 (mt-10) REVERT: A 600 GLU cc_start: 0.8226 (pp20) cc_final: 0.7759 (pp20) REVERT: A 651 LYS cc_start: 0.9003 (tppt) cc_final: 0.8689 (tppt) REVERT: A 663 ASP cc_start: 0.7874 (p0) cc_final: 0.7345 (p0) REVERT: A 691 GLU cc_start: 0.8592 (tp30) cc_final: 0.7870 (tp30) REVERT: A 695 LYS cc_start: 0.8849 (tmtt) cc_final: 0.8564 (tptp) REVERT: A 717 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 730 GLU cc_start: 0.8392 (tp30) cc_final: 0.8170 (tp30) REVERT: A 737 MET cc_start: 0.7541 (ttm) cc_final: 0.7310 (ttm) REVERT: A 751 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 752 LYS cc_start: 0.8961 (tttm) cc_final: 0.8519 (ttmm) REVERT: A 755 LYS cc_start: 0.8861 (ttmt) cc_final: 0.8510 (ttmt) REVERT: A 764 GLU cc_start: 0.7884 (mp0) cc_final: 0.7492 (mp0) REVERT: B 262 GLU cc_start: 0.8526 (tp30) cc_final: 0.8155 (tm-30) REVERT: B 280 ARG cc_start: 0.7431 (mmt-90) cc_final: 0.7181 (mpt180) REVERT: B 297 ARG cc_start: 0.8750 (tpt170) cc_final: 0.8432 (tpt170) REVERT: B 301 ASN cc_start: 0.8816 (t0) cc_final: 0.8479 (t0) REVERT: B 311 ASN cc_start: 0.8038 (t0) cc_final: 0.7783 (t0) REVERT: B 324 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: B 328 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8332 (ttm110) REVERT: B 333 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7638 (tm-30) REVERT: B 346 GLU cc_start: 0.7607 (mp0) cc_final: 0.7351 (mp0) REVERT: B 391 ARG cc_start: 0.8286 (ptt-90) cc_final: 0.7707 (ptt-90) REVERT: B 421 ASP cc_start: 0.8785 (t0) cc_final: 0.8325 (t0) REVERT: B 448 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8219 (mtpt) REVERT: B 461 CYS cc_start: 0.8787 (t) cc_final: 0.8488 (t) REVERT: B 463 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8026 (mm-30) REVERT: B 468 THR cc_start: 0.8760 (m) cc_final: 0.8240 (p) REVERT: B 486 VAL cc_start: 0.8994 (p) cc_final: 0.8744 (m) REVERT: B 490 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7841 (t0) REVERT: B 492 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: B 493 SER cc_start: 0.8951 (t) cc_final: 0.8593 (p) REVERT: B 499 ARG cc_start: 0.7652 (tpm170) cc_final: 0.7247 (tpm170) REVERT: B 512 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7898 (ttpp) REVERT: B 525 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8494 (mmtp) REVERT: B 534 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8660 (tp) REVERT: B 540 GLU cc_start: 0.8051 (pp20) cc_final: 0.7745 (pp20) REVERT: B 556 TYR cc_start: 0.8372 (p90) cc_final: 0.7890 (p90) REVERT: B 582 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8451 (mtmm) REVERT: B 585 GLU cc_start: 0.8304 (pt0) cc_final: 0.7536 (pp20) REVERT: B 587 PHE cc_start: 0.7970 (t80) cc_final: 0.7549 (t80) REVERT: B 600 GLU cc_start: 0.8258 (pp20) cc_final: 0.7734 (pp20) REVERT: B 617 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7869 (mm-30) REVERT: B 638 THR cc_start: 0.8706 (t) cc_final: 0.8416 (p) REVERT: B 642 ASN cc_start: 0.8698 (t0) cc_final: 0.8388 (t0) REVERT: B 643 GLU cc_start: 0.8691 (tp30) cc_final: 0.8199 (tp30) REVERT: B 660 ASN cc_start: 0.8604 (p0) cc_final: 0.7405 (p0) REVERT: B 663 ASP cc_start: 0.8245 (p0) cc_final: 0.7964 (p0) REVERT: B 676 ASP cc_start: 0.8483 (p0) cc_final: 0.8071 (p0) REVERT: B 678 HIS cc_start: 0.8183 (m170) cc_final: 0.7799 (m170) REVERT: B 691 GLU cc_start: 0.8393 (tp30) cc_final: 0.7654 (tp30) REVERT: B 694 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8319 (mtpt) REVERT: B 695 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8390 (tptm) REVERT: B 696 CYS cc_start: 0.8813 (t) cc_final: 0.8496 (t) REVERT: B 723 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: B 751 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7726 (tp30) REVERT: B 755 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8603 (ttmm) REVERT: B 770 GLU cc_start: 0.8562 (tp30) cc_final: 0.8261 (mm-30) REVERT: C 255 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 262 GLU cc_start: 0.8456 (tp30) cc_final: 0.8224 (tm-30) REVERT: C 267 GLN cc_start: 0.8963 (pt0) cc_final: 0.8694 (pt0) REVERT: C 280 ARG cc_start: 0.7897 (mmt180) cc_final: 0.7682 (mmt90) REVERT: C 324 GLU cc_start: 0.7249 (mp0) cc_final: 0.6600 (mp0) REVERT: C 333 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7503 (tp30) REVERT: C 382 LYS cc_start: 0.7457 (mtmt) cc_final: 0.7153 (mtmm) REVERT: C 391 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7738 (mtm-85) REVERT: C 393 ASN cc_start: 0.8718 (m-40) cc_final: 0.8516 (m-40) REVERT: C 406 ASP cc_start: 0.7600 (t0) cc_final: 0.6821 (m-30) REVERT: C 421 ASP cc_start: 0.8611 (t0) cc_final: 0.8257 (t0) REVERT: C 426 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8459 (mm-40) REVERT: C 484 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8149 (mm) REVERT: C 488 LEU cc_start: 0.7834 (tp) cc_final: 0.7165 (tp) REVERT: C 490 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7954 (t0) REVERT: C 492 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: C 493 SER cc_start: 0.8919 (t) cc_final: 0.8631 (p) REVERT: C 495 MET cc_start: 0.8762 (ttp) cc_final: 0.8533 (ttm) REVERT: C 512 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8043 (mmmt) REVERT: C 522 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 525 LYS cc_start: 0.8669 (tppp) cc_final: 0.8312 (tppp) REVERT: C 573 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 582 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8460 (mmmm) REVERT: C 595 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8070 (mt-10) REVERT: C 599 ARG cc_start: 0.8759 (mtt-85) cc_final: 0.8245 (ttm-80) REVERT: C 600 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: C 691 GLU cc_start: 0.8505 (tp30) cc_final: 0.7889 (tp30) REVERT: C 699 LYS cc_start: 0.9087 (tptp) cc_final: 0.8768 (tppt) REVERT: C 710 HIS cc_start: 0.8822 (m90) cc_final: 0.8544 (m-70) REVERT: C 715 ARG cc_start: 0.8516 (ttp-170) cc_final: 0.8260 (ptm160) REVERT: C 730 GLU cc_start: 0.8499 (tp30) cc_final: 0.7993 (mm-30) REVERT: C 751 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7706 (tm-30) REVERT: C 755 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8225 (tmtt) REVERT: C 771 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7545 (pp20) REVERT: D 252 LYS cc_start: 0.8607 (tppp) cc_final: 0.8181 (tppp) REVERT: D 262 GLU cc_start: 0.8385 (tp30) cc_final: 0.8159 (tm-30) REVERT: D 280 ARG cc_start: 0.7919 (mpt180) cc_final: 0.7553 (mmt90) REVERT: D 328 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8530 (ttm110) REVERT: D 333 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7348 (tm-30) REVERT: D 374 MET cc_start: 0.8348 (tpt) cc_final: 0.7875 (tpp) REVERT: D 425 LYS cc_start: 0.8921 (mttm) cc_final: 0.8634 (ttmm) REVERT: D 426 GLN cc_start: 0.8957 (tp40) cc_final: 0.8529 (tp40) REVERT: D 434 ARG cc_start: 0.7407 (mtt90) cc_final: 0.7141 (mtt90) REVERT: D 443 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8415 (mmtp) REVERT: D 444 TYR cc_start: 0.8729 (t80) cc_final: 0.8247 (t80) REVERT: D 448 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8043 (ttmm) REVERT: D 461 CYS cc_start: 0.8660 (m) cc_final: 0.8250 (t) REVERT: D 463 GLU cc_start: 0.8655 (tp30) cc_final: 0.8255 (mm-30) REVERT: D 492 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: D 512 LYS cc_start: 0.8337 (ttmm) cc_final: 0.8079 (ttmm) REVERT: D 513 VAL cc_start: 0.8487 (m) cc_final: 0.8259 (p) REVERT: D 523 GLU cc_start: 0.8116 (tp30) cc_final: 0.7121 (tp30) REVERT: D 525 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8626 (mmmm) REVERT: D 527 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8091 (ttmm) REVERT: D 563 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8166 (mtpt) REVERT: D 600 GLU cc_start: 0.8196 (pp20) cc_final: 0.7740 (pp20) REVERT: D 604 LYS cc_start: 0.8765 (ttpt) cc_final: 0.8541 (ttmt) REVERT: D 642 ASN cc_start: 0.8711 (t0) cc_final: 0.8332 (t0) REVERT: D 717 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8177 (tm-30) REVERT: D 723 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: D 751 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 755 LYS cc_start: 0.8799 (tttt) cc_final: 0.8362 (tptp) REVERT: D 768 TYR cc_start: 0.6920 (m-10) cc_final: 0.6463 (m-10) REVERT: D 771 GLU cc_start: 0.8097 (pp20) cc_final: 0.7671 (pp20) REVERT: E 242 LEU cc_start: 0.8686 (mm) cc_final: 0.8413 (tp) REVERT: E 255 GLU cc_start: 0.8889 (tt0) cc_final: 0.8684 (tt0) REVERT: E 262 GLU cc_start: 0.8527 (tp30) cc_final: 0.8209 (tm-30) REVERT: E 297 ARG cc_start: 0.8645 (tpt90) cc_final: 0.8176 (tpt90) REVERT: E 301 ASN cc_start: 0.8769 (t0) cc_final: 0.8501 (t0) REVERT: E 311 ASN cc_start: 0.7871 (m-40) cc_final: 0.7657 (t0) REVERT: E 382 LYS cc_start: 0.7341 (mtpt) cc_final: 0.7096 (mtpt) REVERT: E 401 ARG cc_start: 0.8053 (mmp80) cc_final: 0.7554 (tpp80) REVERT: E 408 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6641 (tm-30) REVERT: E 410 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: E 443 LYS cc_start: 0.8918 (tppt) cc_final: 0.8465 (tppt) REVERT: E 444 TYR cc_start: 0.8849 (t80) cc_final: 0.8337 (t80) REVERT: E 461 CYS cc_start: 0.8756 (m) cc_final: 0.8389 (t) REVERT: E 490 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8050 (t0) REVERT: E 492 GLU cc_start: 0.8655 (tp30) cc_final: 0.8390 (tp30) REVERT: E 512 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7777 (ttpt) REVERT: E 600 GLU cc_start: 0.8284 (pp20) cc_final: 0.7792 (pp20) REVERT: E 617 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7748 (mm-30) REVERT: E 619 ASP cc_start: 0.8502 (m-30) cc_final: 0.8280 (m-30) REVERT: E 642 ASN cc_start: 0.8609 (t0) cc_final: 0.8366 (t0) REVERT: E 661 ARG cc_start: 0.6812 (tpt90) cc_final: 0.6193 (tpt170) REVERT: E 663 ASP cc_start: 0.8646 (p0) cc_final: 0.8310 (p0) REVERT: E 664 GLU cc_start: 0.8529 (tt0) cc_final: 0.8234 (tt0) REVERT: E 678 HIS cc_start: 0.8197 (m170) cc_final: 0.7772 (m170) REVERT: E 696 CYS cc_start: 0.8761 (t) cc_final: 0.8451 (t) REVERT: E 745 VAL cc_start: 0.8548 (t) cc_final: 0.8074 (m) REVERT: E 751 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7744 (tp30) REVERT: E 752 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8516 (ttmm) REVERT: E 755 LYS cc_start: 0.8811 (tptm) cc_final: 0.8334 (tptm) REVERT: E 770 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8311 (mm-30) REVERT: E 771 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7801 (tm-30) REVERT: F 255 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8093 (tm-30) REVERT: F 262 GLU cc_start: 0.8515 (tp30) cc_final: 0.8235 (tp30) REVERT: F 280 ARG cc_start: 0.7973 (mtt90) cc_final: 0.7668 (mtt180) REVERT: F 311 ASN cc_start: 0.8070 (t0) cc_final: 0.7725 (t0) REVERT: F 333 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7526 (tp30) REVERT: F 335 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8354 (mtp-110) REVERT: F 346 GLU cc_start: 0.7800 (mp0) cc_final: 0.7557 (mp0) REVERT: F 374 MET cc_start: 0.7892 (tpt) cc_final: 0.7684 (tpt) REVERT: F 391 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7757 (mtm-85) REVERT: F 406 ASP cc_start: 0.7013 (t0) cc_final: 0.6751 (m-30) REVERT: F 410 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7483 (tp30) REVERT: F 443 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8500 (mmtt) REVERT: F 444 TYR cc_start: 0.8896 (t80) cc_final: 0.8142 (t80) REVERT: F 468 THR cc_start: 0.8670 (m) cc_final: 0.8116 (p) REVERT: F 488 LEU cc_start: 0.7673 (tp) cc_final: 0.7263 (tt) REVERT: F 490 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7872 (t0) REVERT: F 513 VAL cc_start: 0.8801 (m) cc_final: 0.8432 (p) REVERT: F 522 GLU cc_start: 0.8304 (tp30) cc_final: 0.7885 (mp0) REVERT: F 536 LEU cc_start: 0.9030 (mm) cc_final: 0.8672 (tp) REVERT: F 540 GLU cc_start: 0.7923 (pp20) cc_final: 0.7592 (pp20) REVERT: F 572 THR cc_start: 0.8787 (m) cc_final: 0.8310 (p) REVERT: F 573 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7650 (mm-30) REVERT: F 595 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7793 (mp0) REVERT: F 621 LEU cc_start: 0.7728 (mp) cc_final: 0.7494 (mp) REVERT: F 642 ASN cc_start: 0.8383 (t0) cc_final: 0.8108 (t0) REVERT: F 661 ARG cc_start: 0.7427 (tpt170) cc_final: 0.6521 (tpt170) REVERT: F 687 ASN cc_start: 0.8835 (t0) cc_final: 0.8616 (t0) REVERT: F 691 GLU cc_start: 0.8490 (tp30) cc_final: 0.7753 (tp30) REVERT: F 694 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8735 (mtpp) REVERT: F 697 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8558 (t) REVERT: F 699 LYS cc_start: 0.9118 (tptp) cc_final: 0.8711 (tppp) REVERT: F 729 GLN cc_start: 0.8617 (mt0) cc_final: 0.8286 (mt0) REVERT: F 746 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7713 (mp0) REVERT: F 751 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7625 (tm-30) REVERT: F 754 PHE cc_start: 0.8631 (t80) cc_final: 0.8373 (t80) REVERT: F 755 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8399 (ttmm) outliers start: 107 outliers final: 63 residues processed: 955 average time/residue: 0.1981 time to fit residues: 274.8474 Evaluate side-chains 968 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 887 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 738 GLU Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 486 VAL Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 600 GLU Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 723 GLU Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 83 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 160 optimal weight: 0.0870 chunk 51 optimal weight: 0.6980 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN B 426 GLN B 687 ASN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.134934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112326 restraints weight = 44267.450| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.53 r_work: 0.3324 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25790 Z= 0.134 Angle : 0.660 10.857 34986 Z= 0.325 Chirality : 0.044 0.161 4020 Planarity : 0.005 0.086 4488 Dihedral : 12.216 174.362 3816 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.52 % Allowed : 21.33 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 3240 helix: 1.15 (0.13), residues: 1602 sheet: 0.46 (0.29), residues: 348 loop : -0.09 (0.20), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 775 TYR 0.022 0.001 TYR C 444 PHE 0.030 0.002 PHE B 507 TRP 0.010 0.002 TRP E 515 HIS 0.031 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00307 (25782) covalent geometry : angle 0.65961 (34986) hydrogen bonds : bond 0.03587 ( 1230) hydrogen bonds : angle 4.11601 ( 3498) Misc. bond : bond 0.00080 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 904 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8299 (pm20) cc_final: 0.7902 (pm20) REVERT: A 262 GLU cc_start: 0.8490 (tp30) cc_final: 0.8282 (tp30) REVERT: A 280 ARG cc_start: 0.7831 (mmt90) cc_final: 0.7625 (mpt180) REVERT: A 297 ARG cc_start: 0.8729 (tpt170) cc_final: 0.8343 (tpt170) REVERT: A 324 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 333 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 335 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8345 (mtp-110) REVERT: A 426 GLN cc_start: 0.8962 (tp40) cc_final: 0.8736 (mm-40) REVERT: A 429 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8205 (mmm-85) REVERT: A 443 LYS cc_start: 0.9023 (mmpt) cc_final: 0.8656 (tppt) REVERT: A 444 TYR cc_start: 0.8698 (t80) cc_final: 0.8288 (t80) REVERT: A 448 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8090 (mttp) REVERT: A 453 VAL cc_start: 0.8944 (p) cc_final: 0.8522 (m) REVERT: A 487 THR cc_start: 0.8903 (t) cc_final: 0.8442 (p) REVERT: A 488 LEU cc_start: 0.8114 (tp) cc_final: 0.7597 (tp) REVERT: A 490 ASP cc_start: 0.8282 (t0) cc_final: 0.7834 (t0) REVERT: A 492 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: A 512 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8300 (tttm) REVERT: A 523 GLU cc_start: 0.8249 (tp30) cc_final: 0.7493 (tp30) REVERT: A 537 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: A 540 GLU cc_start: 0.7933 (pp20) cc_final: 0.7502 (pp20) REVERT: A 548 SER cc_start: 0.8845 (m) cc_final: 0.8289 (p) REVERT: A 556 TYR cc_start: 0.8413 (p90) cc_final: 0.8068 (p90) REVERT: A 586 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8502 (tp) REVERT: A 595 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8254 (mp0) REVERT: A 600 GLU cc_start: 0.8208 (pp20) cc_final: 0.7735 (pp20) REVERT: A 651 LYS cc_start: 0.8969 (tppt) cc_final: 0.8675 (tppt) REVERT: A 661 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7212 (mmm160) REVERT: A 663 ASP cc_start: 0.7847 (p0) cc_final: 0.7049 (p0) REVERT: A 691 GLU cc_start: 0.8554 (tp30) cc_final: 0.7931 (tp30) REVERT: A 695 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8566 (tptp) REVERT: A 717 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 730 GLU cc_start: 0.8373 (tp30) cc_final: 0.7940 (mm-30) REVERT: A 737 MET cc_start: 0.7532 (ttm) cc_final: 0.7318 (ttm) REVERT: A 751 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 752 LYS cc_start: 0.8954 (tttm) cc_final: 0.8519 (ttmm) REVERT: A 755 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8511 (ttmt) REVERT: A 764 GLU cc_start: 0.7974 (mp0) cc_final: 0.7631 (mp0) REVERT: B 262 GLU cc_start: 0.8476 (tp30) cc_final: 0.8167 (tm-30) REVERT: B 297 ARG cc_start: 0.8769 (tpt170) cc_final: 0.8453 (tpt170) REVERT: B 301 ASN cc_start: 0.8878 (t0) cc_final: 0.8549 (t0) REVERT: B 311 ASN cc_start: 0.7987 (t0) cc_final: 0.7708 (t0) REVERT: B 324 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: B 328 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8295 (ttm110) REVERT: B 333 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 346 GLU cc_start: 0.7570 (mp0) cc_final: 0.7292 (mp0) REVERT: B 391 ARG cc_start: 0.8261 (ptt-90) cc_final: 0.7726 (ptt-90) REVERT: B 421 ASP cc_start: 0.8789 (t0) cc_final: 0.8297 (t0) REVERT: B 448 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8171 (mtpt) REVERT: B 461 CYS cc_start: 0.8798 (t) cc_final: 0.8520 (t) REVERT: B 463 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 468 THR cc_start: 0.8732 (m) cc_final: 0.8228 (p) REVERT: B 486 VAL cc_start: 0.8968 (p) cc_final: 0.8763 (m) REVERT: B 490 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7825 (t0) REVERT: B 492 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: B 493 SER cc_start: 0.9015 (t) cc_final: 0.8639 (p) REVERT: B 499 ARG cc_start: 0.7584 (tpm170) cc_final: 0.7231 (tpm170) REVERT: B 512 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7952 (ttpp) REVERT: B 525 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8391 (mmtp) REVERT: B 534 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8690 (tp) REVERT: B 540 GLU cc_start: 0.8026 (pp20) cc_final: 0.7781 (pp20) REVERT: B 585 GLU cc_start: 0.8339 (pt0) cc_final: 0.7571 (pp20) REVERT: B 587 PHE cc_start: 0.8004 (t80) cc_final: 0.7591 (t80) REVERT: B 600 GLU cc_start: 0.8269 (pp20) cc_final: 0.7725 (pp20) REVERT: B 617 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7922 (mm-30) REVERT: B 638 THR cc_start: 0.8655 (t) cc_final: 0.8376 (p) REVERT: B 642 ASN cc_start: 0.8641 (t0) cc_final: 0.8325 (t0) REVERT: B 643 GLU cc_start: 0.8717 (tp30) cc_final: 0.8187 (tp30) REVERT: B 660 ASN cc_start: 0.8622 (p0) cc_final: 0.7655 (p0) REVERT: B 663 ASP cc_start: 0.8193 (p0) cc_final: 0.7914 (p0) REVERT: B 676 ASP cc_start: 0.8496 (p0) cc_final: 0.7827 (p0) REVERT: B 678 HIS cc_start: 0.8216 (m170) cc_final: 0.7817 (m170) REVERT: B 691 GLU cc_start: 0.8452 (tp30) cc_final: 0.8058 (tp30) REVERT: B 694 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8380 (mtpt) REVERT: B 695 LYS cc_start: 0.8686 (tmtt) cc_final: 0.8399 (tptm) REVERT: B 696 CYS cc_start: 0.8854 (t) cc_final: 0.8532 (t) REVERT: B 715 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.7821 (ttp80) REVERT: B 723 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: B 751 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7608 (tp30) REVERT: B 755 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8598 (ttmm) REVERT: B 770 GLU cc_start: 0.8533 (tp30) cc_final: 0.8245 (mm-30) REVERT: C 255 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8082 (tm-30) REVERT: C 262 GLU cc_start: 0.8464 (tp30) cc_final: 0.8180 (tm-30) REVERT: C 267 GLN cc_start: 0.8972 (pt0) cc_final: 0.8433 (pt0) REVERT: C 324 GLU cc_start: 0.7309 (mp0) cc_final: 0.6685 (mp0) REVERT: C 333 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7526 (tp30) REVERT: C 382 LYS cc_start: 0.7432 (mtmt) cc_final: 0.7122 (mtmm) REVERT: C 391 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: C 393 ASN cc_start: 0.8679 (m-40) cc_final: 0.8443 (m-40) REVERT: C 401 ARG cc_start: 0.7915 (mmp80) cc_final: 0.7588 (tpp80) REVERT: C 406 ASP cc_start: 0.7533 (t0) cc_final: 0.6892 (m-30) REVERT: C 421 ASP cc_start: 0.8499 (t0) cc_final: 0.7918 (t0) REVERT: C 425 LYS cc_start: 0.8960 (mttp) cc_final: 0.8671 (mttp) REVERT: C 426 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8478 (mm-40) REVERT: C 453 VAL cc_start: 0.8883 (p) cc_final: 0.8580 (m) REVERT: C 484 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8153 (mm) REVERT: C 488 LEU cc_start: 0.7809 (tp) cc_final: 0.7099 (tp) REVERT: C 490 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7905 (t0) REVERT: C 492 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: C 493 SER cc_start: 0.8906 (t) cc_final: 0.8616 (p) REVERT: C 495 MET cc_start: 0.8744 (ttp) cc_final: 0.8498 (ttm) REVERT: C 512 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8017 (mmmt) REVERT: C 522 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8010 (mm-30) REVERT: C 525 LYS cc_start: 0.8670 (tppp) cc_final: 0.8324 (tppp) REVERT: C 540 GLU cc_start: 0.7996 (pp20) cc_final: 0.7637 (pp20) REVERT: C 582 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8486 (mmmm) REVERT: C 595 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8031 (mt-10) REVERT: C 599 ARG cc_start: 0.8780 (mtt-85) cc_final: 0.8371 (mtt-85) REVERT: C 600 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: C 645 ASP cc_start: 0.8269 (t0) cc_final: 0.8059 (t0) REVERT: C 666 ASP cc_start: 0.8337 (t0) cc_final: 0.7574 (p0) REVERT: C 676 ASP cc_start: 0.8527 (p0) cc_final: 0.8039 (p0) REVERT: C 691 GLU cc_start: 0.8547 (tp30) cc_final: 0.7945 (tp30) REVERT: C 699 LYS cc_start: 0.9066 (tptp) cc_final: 0.8743 (tppt) REVERT: C 710 HIS cc_start: 0.8832 (m90) cc_final: 0.8526 (m-70) REVERT: C 730 GLU cc_start: 0.8464 (tp30) cc_final: 0.7668 (mm-30) REVERT: C 751 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7733 (tm-30) REVERT: C 755 LYS cc_start: 0.8580 (tmtt) cc_final: 0.8202 (tmtt) REVERT: D 252 LYS cc_start: 0.8584 (tppp) cc_final: 0.8162 (tppp) REVERT: D 262 GLU cc_start: 0.8380 (tp30) cc_final: 0.8161 (tm-30) REVERT: D 280 ARG cc_start: 0.7979 (mpt180) cc_final: 0.7572 (mmt90) REVERT: D 328 ARG cc_start: 0.8739 (ttm110) cc_final: 0.8178 (ttm110) REVERT: D 333 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 374 MET cc_start: 0.8346 (tpt) cc_final: 0.7887 (tpp) REVERT: D 425 LYS cc_start: 0.8982 (mttm) cc_final: 0.8636 (ttmm) REVERT: D 426 GLN cc_start: 0.8947 (tp40) cc_final: 0.8524 (tp40) REVERT: D 428 SER cc_start: 0.9038 (m) cc_final: 0.8729 (p) REVERT: D 434 ARG cc_start: 0.7474 (mtt90) cc_final: 0.7071 (mtt90) REVERT: D 443 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8429 (mmtp) REVERT: D 444 TYR cc_start: 0.8679 (t80) cc_final: 0.8271 (t80) REVERT: D 448 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8065 (ttmm) REVERT: D 461 CYS cc_start: 0.8692 (m) cc_final: 0.8290 (t) REVERT: D 463 GLU cc_start: 0.8706 (tp30) cc_final: 0.8329 (mm-30) REVERT: D 488 LEU cc_start: 0.8027 (tp) cc_final: 0.7728 (tt) REVERT: D 492 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: D 512 LYS cc_start: 0.8372 (ttmm) cc_final: 0.8108 (ttmm) REVERT: D 513 VAL cc_start: 0.8433 (m) cc_final: 0.8181 (p) REVERT: D 523 GLU cc_start: 0.8162 (tp30) cc_final: 0.7158 (tp30) REVERT: D 525 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8692 (mmmm) REVERT: D 527 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8144 (ttmm) REVERT: D 537 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: D 563 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8133 (mtpt) REVERT: D 600 GLU cc_start: 0.8208 (pp20) cc_final: 0.7785 (pp20) REVERT: D 604 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8472 (ttmt) REVERT: D 642 ASN cc_start: 0.8727 (t0) cc_final: 0.8351 (t0) REVERT: D 661 ARG cc_start: 0.7016 (tpt170) cc_final: 0.6553 (tpt170) REVERT: D 717 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 723 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: D 751 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7622 (tm-30) REVERT: D 755 LYS cc_start: 0.8755 (tttt) cc_final: 0.8331 (tptp) REVERT: D 768 TYR cc_start: 0.6925 (m-10) cc_final: 0.6496 (m-10) REVERT: D 771 GLU cc_start: 0.8123 (pp20) cc_final: 0.7630 (pp20) REVERT: D 775 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7200 (ttp80) REVERT: E 262 GLU cc_start: 0.8532 (tp30) cc_final: 0.8209 (tm-30) REVERT: E 297 ARG cc_start: 0.8684 (tpt90) cc_final: 0.8258 (tpt90) REVERT: E 301 ASN cc_start: 0.8843 (t0) cc_final: 0.8576 (t0) REVERT: E 311 ASN cc_start: 0.7860 (m-40) cc_final: 0.7641 (t0) REVERT: E 382 LYS cc_start: 0.7440 (mtpt) cc_final: 0.7163 (mtpt) REVERT: E 401 ARG cc_start: 0.7958 (mmp80) cc_final: 0.7455 (tpp80) REVERT: E 410 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7644 (mm-30) REVERT: E 443 LYS cc_start: 0.8937 (tppt) cc_final: 0.8488 (tppt) REVERT: E 444 TYR cc_start: 0.8790 (t80) cc_final: 0.8372 (t80) REVERT: E 461 CYS cc_start: 0.8809 (m) cc_final: 0.8441 (t) REVERT: E 490 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8032 (t0) REVERT: E 512 LYS cc_start: 0.8450 (ttpt) cc_final: 0.7793 (ttpt) REVERT: E 600 GLU cc_start: 0.8318 (pp20) cc_final: 0.7820 (pp20) REVERT: E 617 GLU cc_start: 0.8646 (mt-10) cc_final: 0.7829 (mm-30) REVERT: E 619 ASP cc_start: 0.8558 (m-30) cc_final: 0.8330 (m-30) REVERT: E 642 ASN cc_start: 0.8647 (t0) cc_final: 0.8401 (t0) REVERT: E 661 ARG cc_start: 0.6668 (tpt90) cc_final: 0.6053 (tpt170) REVERT: E 663 ASP cc_start: 0.8674 (p0) cc_final: 0.8277 (p0) REVERT: E 664 GLU cc_start: 0.8528 (tt0) cc_final: 0.8203 (tt0) REVERT: E 678 HIS cc_start: 0.8189 (m170) cc_final: 0.7820 (m170) REVERT: E 696 CYS cc_start: 0.8751 (t) cc_final: 0.8442 (t) REVERT: E 745 VAL cc_start: 0.8545 (t) cc_final: 0.8084 (m) REVERT: E 751 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7584 (tp30) REVERT: E 752 LYS cc_start: 0.8866 (tmtt) cc_final: 0.8513 (ttmm) REVERT: E 755 LYS cc_start: 0.8798 (tptm) cc_final: 0.8209 (tptm) REVERT: E 770 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8299 (mm-30) REVERT: E 771 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7842 (tm-30) REVERT: F 253 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: F 255 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8080 (tm-30) REVERT: F 262 GLU cc_start: 0.8588 (tp30) cc_final: 0.8221 (tp30) REVERT: F 267 GLN cc_start: 0.8825 (pt0) cc_final: 0.8580 (pt0) REVERT: F 280 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7664 (mtt180) REVERT: F 285 HIS cc_start: 0.7867 (m-70) cc_final: 0.7276 (m-70) REVERT: F 311 ASN cc_start: 0.8047 (t0) cc_final: 0.7714 (t0) REVERT: F 333 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7567 (tp30) REVERT: F 346 GLU cc_start: 0.7789 (mp0) cc_final: 0.7542 (mp0) REVERT: F 374 MET cc_start: 0.7876 (tpt) cc_final: 0.7612 (tpt) REVERT: F 391 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7471 (mtm180) REVERT: F 406 ASP cc_start: 0.7366 (t0) cc_final: 0.6652 (m-30) REVERT: F 443 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8366 (mmtt) REVERT: F 444 TYR cc_start: 0.8884 (t80) cc_final: 0.8142 (t80) REVERT: F 468 THR cc_start: 0.8692 (m) cc_final: 0.8046 (p) REVERT: F 488 LEU cc_start: 0.7656 (tp) cc_final: 0.7224 (tt) REVERT: F 490 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7875 (t0) REVERT: F 513 VAL cc_start: 0.8780 (m) cc_final: 0.8405 (p) REVERT: F 522 GLU cc_start: 0.8313 (tp30) cc_final: 0.7905 (mp0) REVERT: F 536 LEU cc_start: 0.9037 (mm) cc_final: 0.8668 (tp) REVERT: F 540 GLU cc_start: 0.7934 (pp20) cc_final: 0.7595 (pp20) REVERT: F 572 THR cc_start: 0.8792 (m) cc_final: 0.8337 (p) REVERT: F 573 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7627 (mm-30) REVERT: F 595 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7776 (mp0) REVERT: F 642 ASN cc_start: 0.8393 (t0) cc_final: 0.8124 (t0) REVERT: F 661 ARG cc_start: 0.7406 (tpt170) cc_final: 0.7063 (tpt170) REVERT: F 691 GLU cc_start: 0.8528 (tp30) cc_final: 0.7753 (tp30) REVERT: F 697 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8540 (t) REVERT: F 729 GLN cc_start: 0.8563 (mt0) cc_final: 0.8231 (mt0) REVERT: F 746 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7667 (mp0) REVERT: F 751 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7609 (tm-30) REVERT: F 754 PHE cc_start: 0.8592 (t80) cc_final: 0.8326 (t80) REVERT: F 755 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8359 (ttmm) outliers start: 122 outliers final: 73 residues processed: 952 average time/residue: 0.1981 time to fit residues: 273.8718 Evaluate side-chains 985 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 889 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 443 LYS Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 645 ASP Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 738 GLU Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 531 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 600 GLU Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 697 THR Chi-restraints excluded: chain F residue 723 GLU Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 228 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 67 optimal weight: 6.9990 chunk 312 optimal weight: 4.9990 chunk 178 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 393 ASN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.135252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112511 restraints weight = 44631.143| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.56 r_work: 0.3326 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25790 Z= 0.137 Angle : 0.673 9.779 34986 Z= 0.328 Chirality : 0.044 0.196 4020 Planarity : 0.005 0.088 4488 Dihedral : 12.075 166.849 3816 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.00 % Allowed : 22.19 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 3240 helix: 1.21 (0.13), residues: 1596 sheet: 0.51 (0.29), residues: 348 loop : -0.10 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 775 TYR 0.020 0.001 TYR C 444 PHE 0.027 0.002 PHE B 507 TRP 0.011 0.002 TRP C 515 HIS 0.008 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00318 (25782) covalent geometry : angle 0.67301 (34986) hydrogen bonds : bond 0.03524 ( 1230) hydrogen bonds : angle 4.08614 ( 3498) Misc. bond : bond 0.00076 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 890 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.8320 (tp30) cc_final: 0.7802 (tm-30) REVERT: A 253 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: A 255 GLU cc_start: 0.8767 (tt0) cc_final: 0.8375 (tm-30) REVERT: A 262 GLU cc_start: 0.8529 (tp30) cc_final: 0.8317 (tp30) REVERT: A 297 ARG cc_start: 0.8761 (tpt170) cc_final: 0.8427 (tpt170) REVERT: A 333 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7472 (tm-30) REVERT: A 335 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8376 (mtp-110) REVERT: A 382 LYS cc_start: 0.7480 (mtmt) cc_final: 0.7036 (mmmt) REVERT: A 408 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 426 GLN cc_start: 0.8969 (tp40) cc_final: 0.8740 (mm-40) REVERT: A 429 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.8214 (mmm-85) REVERT: A 443 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8671 (tppt) REVERT: A 444 TYR cc_start: 0.8695 (t80) cc_final: 0.8267 (t80) REVERT: A 448 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8126 (mttp) REVERT: A 453 VAL cc_start: 0.8907 (p) cc_final: 0.8506 (m) REVERT: A 463 GLU cc_start: 0.8607 (tp30) cc_final: 0.8088 (tp30) REVERT: A 487 THR cc_start: 0.8928 (t) cc_final: 0.8518 (p) REVERT: A 488 LEU cc_start: 0.8123 (tp) cc_final: 0.7606 (tp) REVERT: A 492 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: A 512 LYS cc_start: 0.8534 (ttmm) cc_final: 0.8237 (tttp) REVERT: A 523 GLU cc_start: 0.8269 (tp30) cc_final: 0.7500 (tp30) REVERT: A 540 GLU cc_start: 0.7926 (pp20) cc_final: 0.7489 (pp20) REVERT: A 548 SER cc_start: 0.8878 (m) cc_final: 0.8374 (p) REVERT: A 556 TYR cc_start: 0.8425 (p90) cc_final: 0.8084 (p90) REVERT: A 585 GLU cc_start: 0.7987 (pt0) cc_final: 0.7490 (pp20) REVERT: A 586 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8259 (tp) REVERT: A 595 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8125 (mm-30) REVERT: A 600 GLU cc_start: 0.8238 (pp20) cc_final: 0.7754 (pp20) REVERT: A 651 LYS cc_start: 0.8949 (tppt) cc_final: 0.8675 (tppt) REVERT: A 661 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7065 (mmm160) REVERT: A 663 ASP cc_start: 0.7785 (p0) cc_final: 0.6797 (p0) REVERT: A 695 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8567 (tptp) REVERT: A 723 GLU cc_start: 0.8269 (mp0) cc_final: 0.8056 (mm-30) REVERT: A 737 MET cc_start: 0.7523 (ttm) cc_final: 0.7276 (ttm) REVERT: A 738 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7955 (tp30) REVERT: A 751 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7266 (tp30) REVERT: A 752 LYS cc_start: 0.8951 (tttm) cc_final: 0.8632 (ttmm) REVERT: A 755 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8484 (ttmt) REVERT: A 764 GLU cc_start: 0.7902 (mp0) cc_final: 0.7556 (mp0) REVERT: B 262 GLU cc_start: 0.8487 (tp30) cc_final: 0.8182 (tm-30) REVERT: B 297 ARG cc_start: 0.8800 (tpt170) cc_final: 0.8483 (tpt170) REVERT: B 301 ASN cc_start: 0.8842 (t0) cc_final: 0.8542 (t0) REVERT: B 311 ASN cc_start: 0.7979 (t0) cc_final: 0.7721 (t0) REVERT: B 324 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: B 328 ARG cc_start: 0.8631 (ttm110) cc_final: 0.8300 (ttm110) REVERT: B 333 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 346 GLU cc_start: 0.7582 (mp0) cc_final: 0.7278 (mp0) REVERT: B 391 ARG cc_start: 0.8270 (ptt-90) cc_final: 0.7747 (ptt-90) REVERT: B 421 ASP cc_start: 0.8811 (t0) cc_final: 0.8287 (t0) REVERT: B 448 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8153 (mtpt) REVERT: B 461 CYS cc_start: 0.8815 (t) cc_final: 0.8597 (t) REVERT: B 463 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8102 (mm-30) REVERT: B 468 THR cc_start: 0.8747 (m) cc_final: 0.8225 (p) REVERT: B 484 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8331 (mm) REVERT: B 486 VAL cc_start: 0.8964 (p) cc_final: 0.8722 (m) REVERT: B 490 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.7959 (t0) REVERT: B 492 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: B 493 SER cc_start: 0.9003 (t) cc_final: 0.8640 (p) REVERT: B 497 ASP cc_start: 0.8152 (t0) cc_final: 0.7671 (t0) REVERT: B 512 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7837 (ttpp) REVERT: B 525 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8372 (mmtp) REVERT: B 534 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8662 (tp) REVERT: B 540 GLU cc_start: 0.8010 (pp20) cc_final: 0.7744 (pp20) REVERT: B 582 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8459 (mtmm) REVERT: B 585 GLU cc_start: 0.8318 (pt0) cc_final: 0.7550 (pp20) REVERT: B 587 PHE cc_start: 0.7958 (t80) cc_final: 0.7573 (t80) REVERT: B 600 GLU cc_start: 0.8220 (pp20) cc_final: 0.7648 (pp20) REVERT: B 617 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7989 (mm-30) REVERT: B 638 THR cc_start: 0.8686 (t) cc_final: 0.8361 (p) REVERT: B 642 ASN cc_start: 0.8637 (t0) cc_final: 0.8335 (t0) REVERT: B 643 GLU cc_start: 0.8673 (tp30) cc_final: 0.8159 (tp30) REVERT: B 660 ASN cc_start: 0.8665 (p0) cc_final: 0.7960 (p0) REVERT: B 663 ASP cc_start: 0.8172 (p0) cc_final: 0.7865 (p0) REVERT: B 666 ASP cc_start: 0.8329 (t0) cc_final: 0.7781 (p0) REVERT: B 677 ARG cc_start: 0.8110 (mmt-90) cc_final: 0.7613 (tpp80) REVERT: B 678 HIS cc_start: 0.8246 (m170) cc_final: 0.7850 (m170) REVERT: B 694 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8423 (mtpt) REVERT: B 695 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8391 (tptp) REVERT: B 696 CYS cc_start: 0.8868 (t) cc_final: 0.8121 (p) REVERT: B 708 ASP cc_start: 0.8288 (p0) cc_final: 0.7813 (p0) REVERT: B 723 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: B 751 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7576 (tp30) REVERT: B 755 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8621 (ttmm) REVERT: B 770 GLU cc_start: 0.8541 (tp30) cc_final: 0.8243 (mm-30) REVERT: C 255 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 262 GLU cc_start: 0.8450 (tp30) cc_final: 0.8151 (tm-30) REVERT: C 267 GLN cc_start: 0.8965 (pt0) cc_final: 0.8465 (pt0) REVERT: C 297 ARG cc_start: 0.8343 (tpt170) cc_final: 0.7833 (tpt170) REVERT: C 324 GLU cc_start: 0.7253 (mp0) cc_final: 0.6619 (mp0) REVERT: C 333 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7562 (tp30) REVERT: C 382 LYS cc_start: 0.7425 (mtmt) cc_final: 0.7115 (mtmm) REVERT: C 391 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: C 406 ASP cc_start: 0.7557 (t0) cc_final: 0.6911 (m-30) REVERT: C 421 ASP cc_start: 0.8518 (t0) cc_final: 0.8126 (t0) REVERT: C 426 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8496 (mm-40) REVERT: C 453 VAL cc_start: 0.8921 (p) cc_final: 0.8628 (m) REVERT: C 484 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8151 (mm) REVERT: C 488 LEU cc_start: 0.7877 (tp) cc_final: 0.7155 (tp) REVERT: C 490 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7900 (t0) REVERT: C 492 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: C 493 SER cc_start: 0.8928 (t) cc_final: 0.8660 (p) REVERT: C 495 MET cc_start: 0.8709 (ttp) cc_final: 0.8457 (ttm) REVERT: C 497 ASP cc_start: 0.8152 (t0) cc_final: 0.7948 (t0) REVERT: C 512 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8010 (mmmt) REVERT: C 522 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 525 LYS cc_start: 0.8687 (tppp) cc_final: 0.8349 (tppp) REVERT: C 540 GLU cc_start: 0.7973 (pp20) cc_final: 0.7608 (pp20) REVERT: C 582 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8476 (mmmm) REVERT: C 595 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8026 (mt-10) REVERT: C 599 ARG cc_start: 0.8768 (mtt-85) cc_final: 0.8371 (mtt-85) REVERT: C 600 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: C 645 ASP cc_start: 0.8270 (t0) cc_final: 0.8053 (t0) REVERT: C 676 ASP cc_start: 0.8522 (p0) cc_final: 0.7830 (p0) REVERT: C 685 ASP cc_start: 0.8138 (p0) cc_final: 0.7922 (p0) REVERT: C 691 GLU cc_start: 0.8552 (tp30) cc_final: 0.8005 (tp30) REVERT: C 699 LYS cc_start: 0.9047 (tptp) cc_final: 0.8725 (tppt) REVERT: C 730 GLU cc_start: 0.8458 (tp30) cc_final: 0.7715 (mm-30) REVERT: C 751 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 755 LYS cc_start: 0.8570 (tmtt) cc_final: 0.8201 (tmtt) REVERT: C 771 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7450 (pp20) REVERT: D 252 LYS cc_start: 0.8564 (tppp) cc_final: 0.8113 (tppp) REVERT: D 280 ARG cc_start: 0.7983 (mpt180) cc_final: 0.7559 (mpt-90) REVERT: D 328 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8196 (ttm110) REVERT: D 333 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7399 (tm-30) REVERT: D 374 MET cc_start: 0.8332 (tpt) cc_final: 0.7896 (tpp) REVERT: D 425 LYS cc_start: 0.8976 (mttm) cc_final: 0.8625 (ttmm) REVERT: D 426 GLN cc_start: 0.8965 (tp40) cc_final: 0.8558 (tp40) REVERT: D 428 SER cc_start: 0.9040 (m) cc_final: 0.8737 (p) REVERT: D 434 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7252 (mtt90) REVERT: D 443 LYS cc_start: 0.8782 (mmtp) cc_final: 0.8421 (mmtp) REVERT: D 444 TYR cc_start: 0.8667 (t80) cc_final: 0.8266 (t80) REVERT: D 448 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8034 (ttmm) REVERT: D 461 CYS cc_start: 0.8662 (m) cc_final: 0.8292 (t) REVERT: D 463 GLU cc_start: 0.8693 (tp30) cc_final: 0.8412 (mm-30) REVERT: D 488 LEU cc_start: 0.8012 (tp) cc_final: 0.7661 (tt) REVERT: D 490 ASP cc_start: 0.8135 (t0) cc_final: 0.7794 (t0) REVERT: D 492 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: D 512 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8086 (ttmm) REVERT: D 513 VAL cc_start: 0.8440 (m) cc_final: 0.8172 (p) REVERT: D 523 GLU cc_start: 0.8143 (tp30) cc_final: 0.7127 (tp30) REVERT: D 525 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8669 (mmmm) REVERT: D 527 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8125 (ttmm) REVERT: D 537 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: D 563 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8147 (mtpt) REVERT: D 600 GLU cc_start: 0.8220 (pp20) cc_final: 0.7748 (pp20) REVERT: D 604 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8483 (ttmt) REVERT: D 642 ASN cc_start: 0.8746 (t0) cc_final: 0.8372 (t0) REVERT: D 661 ARG cc_start: 0.7099 (tpt170) cc_final: 0.6627 (tpt170) REVERT: D 717 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8137 (tm-30) REVERT: D 723 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: D 730 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8290 (mm-30) REVERT: D 751 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7665 (tm-30) REVERT: D 752 LYS cc_start: 0.8819 (tptp) cc_final: 0.8346 (tptp) REVERT: D 755 LYS cc_start: 0.8729 (tttt) cc_final: 0.8274 (tptp) REVERT: D 768 TYR cc_start: 0.6958 (m-10) cc_final: 0.6534 (m-10) REVERT: D 771 GLU cc_start: 0.8152 (pp20) cc_final: 0.7709 (pp20) REVERT: E 242 LEU cc_start: 0.8765 (mm) cc_final: 0.8509 (tp) REVERT: E 262 GLU cc_start: 0.8528 (tp30) cc_final: 0.8239 (tm-30) REVERT: E 297 ARG cc_start: 0.8664 (tpt90) cc_final: 0.8285 (tpt90) REVERT: E 301 ASN cc_start: 0.8870 (t0) cc_final: 0.8601 (t0) REVERT: E 311 ASN cc_start: 0.7796 (m-40) cc_final: 0.7586 (t0) REVERT: E 382 LYS cc_start: 0.7431 (mtpt) cc_final: 0.7126 (mtpt) REVERT: E 401 ARG cc_start: 0.8013 (mmp80) cc_final: 0.7456 (tpp80) REVERT: E 410 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: E 443 LYS cc_start: 0.8956 (tppt) cc_final: 0.8495 (tppt) REVERT: E 444 TYR cc_start: 0.8784 (t80) cc_final: 0.8336 (t80) REVERT: E 461 CYS cc_start: 0.8792 (m) cc_final: 0.8440 (t) REVERT: E 490 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8051 (t0) REVERT: E 512 LYS cc_start: 0.8442 (ttpt) cc_final: 0.7833 (ttpt) REVERT: E 600 GLU cc_start: 0.8350 (pp20) cc_final: 0.7846 (pp20) REVERT: E 642 ASN cc_start: 0.8659 (t0) cc_final: 0.8357 (t0) REVERT: E 661 ARG cc_start: 0.6658 (tpt90) cc_final: 0.6339 (tpt170) REVERT: E 664 GLU cc_start: 0.8511 (tt0) cc_final: 0.8167 (tt0) REVERT: E 676 ASP cc_start: 0.8491 (p0) cc_final: 0.8204 (p0) REVERT: E 678 HIS cc_start: 0.8231 (m170) cc_final: 0.7836 (m170) REVERT: E 694 LYS cc_start: 0.8886 (mttt) cc_final: 0.8300 (mtpp) REVERT: E 696 CYS cc_start: 0.8714 (t) cc_final: 0.8374 (t) REVERT: E 745 VAL cc_start: 0.8542 (t) cc_final: 0.8089 (m) REVERT: E 751 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7526 (tp30) REVERT: E 752 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8502 (ttmm) REVERT: E 755 LYS cc_start: 0.8741 (tptm) cc_final: 0.8287 (tptm) REVERT: E 770 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8311 (mm-30) REVERT: E 771 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7810 (tm-30) REVERT: F 253 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: F 255 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8100 (tm-30) REVERT: F 262 GLU cc_start: 0.8559 (tp30) cc_final: 0.8188 (tp30) REVERT: F 267 GLN cc_start: 0.8803 (pt0) cc_final: 0.8553 (pt0) REVERT: F 311 ASN cc_start: 0.8040 (t0) cc_final: 0.7673 (t0) REVERT: F 333 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7567 (tp30) REVERT: F 335 ARG cc_start: 0.8638 (mtp85) cc_final: 0.8350 (mtp-110) REVERT: F 346 GLU cc_start: 0.7765 (mp0) cc_final: 0.7517 (mp0) REVERT: F 374 MET cc_start: 0.7854 (tpt) cc_final: 0.7585 (tpt) REVERT: F 391 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7693 (mtm-85) REVERT: F 406 ASP cc_start: 0.7347 (t0) cc_final: 0.6651 (m-30) REVERT: F 443 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8508 (tppt) REVERT: F 444 TYR cc_start: 0.8844 (t80) cc_final: 0.8104 (t80) REVERT: F 468 THR cc_start: 0.8561 (m) cc_final: 0.8073 (p) REVERT: F 488 LEU cc_start: 0.7641 (tp) cc_final: 0.7188 (tt) REVERT: F 490 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8028 (t0) REVERT: F 512 LYS cc_start: 0.8515 (tppp) cc_final: 0.8188 (tppp) REVERT: F 513 VAL cc_start: 0.8787 (m) cc_final: 0.8421 (p) REVERT: F 522 GLU cc_start: 0.8349 (tp30) cc_final: 0.7922 (mp0) REVERT: F 536 LEU cc_start: 0.9046 (mm) cc_final: 0.8676 (tp) REVERT: F 540 GLU cc_start: 0.7969 (pp20) cc_final: 0.7629 (pp20) REVERT: F 572 THR cc_start: 0.8790 (m) cc_final: 0.8332 (p) REVERT: F 573 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7612 (mm-30) REVERT: F 595 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7805 (mp0) REVERT: F 621 LEU cc_start: 0.7737 (mt) cc_final: 0.7479 (mp) REVERT: F 642 ASN cc_start: 0.8388 (t0) cc_final: 0.8126 (t0) REVERT: F 661 ARG cc_start: 0.7336 (tpt170) cc_final: 0.6442 (tpt90) REVERT: F 691 GLU cc_start: 0.8501 (tp30) cc_final: 0.7733 (tp30) REVERT: F 729 GLN cc_start: 0.8578 (mt0) cc_final: 0.8262 (mt0) REVERT: F 746 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7689 (mp0) REVERT: F 751 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7550 (tm-30) REVERT: F 754 PHE cc_start: 0.8590 (t80) cc_final: 0.8352 (t80) REVERT: F 755 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8359 (ttmm) outliers start: 108 outliers final: 66 residues processed: 937 average time/residue: 0.2040 time to fit residues: 277.7339 Evaluate side-chains 964 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 873 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 443 LYS Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 738 GLU Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 723 GLU Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 36 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 319 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 HIS ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN ** D 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.137049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115045 restraints weight = 44279.317| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.51 r_work: 0.3327 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25790 Z= 0.141 Angle : 0.690 10.859 34986 Z= 0.335 Chirality : 0.044 0.165 4020 Planarity : 0.005 0.091 4488 Dihedral : 11.974 161.579 3816 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.11 % Allowed : 22.78 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 3240 helix: 1.22 (0.13), residues: 1596 sheet: 0.53 (0.29), residues: 348 loop : -0.07 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 775 TYR 0.022 0.001 TYR C 444 PHE 0.031 0.002 PHE B 754 TRP 0.012 0.002 TRP E 515 HIS 0.011 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00327 (25782) covalent geometry : angle 0.68972 (34986) hydrogen bonds : bond 0.03493 ( 1230) hydrogen bonds : angle 4.08852 ( 3498) Misc. bond : bond 0.00077 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 886 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.8308 (tp30) cc_final: 0.7837 (tm-30) REVERT: A 253 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: A 255 GLU cc_start: 0.8747 (tt0) cc_final: 0.8372 (tm-30) REVERT: A 280 ARG cc_start: 0.7652 (mmt90) cc_final: 0.7415 (mpt180) REVERT: A 297 ARG cc_start: 0.8754 (tpt170) cc_final: 0.8428 (tpt170) REVERT: A 324 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: A 328 ARG cc_start: 0.8737 (ttm110) cc_final: 0.8387 (ttm110) REVERT: A 333 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 335 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8385 (mtp-110) REVERT: A 382 LYS cc_start: 0.7426 (mtmt) cc_final: 0.6996 (mmmt) REVERT: A 426 GLN cc_start: 0.8959 (tp40) cc_final: 0.8748 (mm-40) REVERT: A 443 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8663 (tppt) REVERT: A 444 TYR cc_start: 0.8664 (t80) cc_final: 0.8252 (t80) REVERT: A 448 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8124 (mttp) REVERT: A 453 VAL cc_start: 0.8914 (p) cc_final: 0.8521 (m) REVERT: A 487 THR cc_start: 0.8931 (t) cc_final: 0.8513 (p) REVERT: A 488 LEU cc_start: 0.8113 (tp) cc_final: 0.7587 (tp) REVERT: A 490 ASP cc_start: 0.8349 (t0) cc_final: 0.7875 (t0) REVERT: A 492 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: A 512 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8142 (tttm) REVERT: A 523 GLU cc_start: 0.8292 (tp30) cc_final: 0.7531 (tp30) REVERT: A 537 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: A 540 GLU cc_start: 0.7916 (pp20) cc_final: 0.7502 (pp20) REVERT: A 548 SER cc_start: 0.8864 (m) cc_final: 0.8375 (p) REVERT: A 556 TYR cc_start: 0.8430 (p90) cc_final: 0.8061 (p90) REVERT: A 585 GLU cc_start: 0.7993 (pt0) cc_final: 0.7514 (pp20) REVERT: A 586 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8234 (tp) REVERT: A 595 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8079 (mm-30) REVERT: A 600 GLU cc_start: 0.8245 (pp20) cc_final: 0.7725 (pp20) REVERT: A 651 LYS cc_start: 0.8942 (tppt) cc_final: 0.8668 (tppt) REVERT: A 661 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7049 (mmm160) REVERT: A 663 ASP cc_start: 0.7786 (p0) cc_final: 0.6729 (p0) REVERT: A 695 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8545 (tptp) REVERT: A 717 GLU cc_start: 0.8424 (tp30) cc_final: 0.8099 (tp30) REVERT: A 737 MET cc_start: 0.7564 (ttm) cc_final: 0.7325 (ttm) REVERT: A 751 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7283 (tp30) REVERT: A 752 LYS cc_start: 0.8979 (tttm) cc_final: 0.8644 (ttmm) REVERT: A 755 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8492 (ttmt) REVERT: A 764 GLU cc_start: 0.7927 (mp0) cc_final: 0.7600 (mp0) REVERT: B 262 GLU cc_start: 0.8480 (tp30) cc_final: 0.8266 (tp30) REVERT: B 280 ARG cc_start: 0.7340 (mmt-90) cc_final: 0.6916 (mpt180) REVERT: B 297 ARG cc_start: 0.8773 (tpt170) cc_final: 0.8469 (tpt170) REVERT: B 301 ASN cc_start: 0.8816 (t0) cc_final: 0.8522 (t0) REVERT: B 311 ASN cc_start: 0.7949 (t0) cc_final: 0.7686 (t0) REVERT: B 324 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: B 328 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8293 (ttm110) REVERT: B 333 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7652 (tm-30) REVERT: B 346 GLU cc_start: 0.7556 (mp0) cc_final: 0.7274 (mp0) REVERT: B 421 ASP cc_start: 0.8798 (t0) cc_final: 0.8269 (t0) REVERT: B 443 LYS cc_start: 0.8968 (tppt) cc_final: 0.8519 (tppt) REVERT: B 448 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8196 (mtpt) REVERT: B 461 CYS cc_start: 0.8794 (t) cc_final: 0.8536 (t) REVERT: B 468 THR cc_start: 0.8733 (m) cc_final: 0.8146 (p) REVERT: B 484 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 486 VAL cc_start: 0.8901 (p) cc_final: 0.8640 (m) REVERT: B 490 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 492 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: B 493 SER cc_start: 0.9014 (t) cc_final: 0.8647 (p) REVERT: B 497 ASP cc_start: 0.8186 (t0) cc_final: 0.7742 (t0) REVERT: B 512 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7772 (ttpp) REVERT: B 525 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8414 (mmtp) REVERT: B 534 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 540 GLU cc_start: 0.7963 (pp20) cc_final: 0.7709 (pp20) REVERT: B 556 TYR cc_start: 0.8400 (p90) cc_final: 0.8043 (p90) REVERT: B 582 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8516 (mtmm) REVERT: B 585 GLU cc_start: 0.8301 (pt0) cc_final: 0.7545 (pp20) REVERT: B 587 PHE cc_start: 0.7931 (t80) cc_final: 0.7567 (t80) REVERT: B 600 GLU cc_start: 0.8209 (pp20) cc_final: 0.7635 (pp20) REVERT: B 617 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7947 (mm-30) REVERT: B 638 THR cc_start: 0.8699 (t) cc_final: 0.8385 (p) REVERT: B 642 ASN cc_start: 0.8559 (t0) cc_final: 0.8261 (t0) REVERT: B 643 GLU cc_start: 0.8685 (tp30) cc_final: 0.8161 (tp30) REVERT: B 660 ASN cc_start: 0.8731 (p0) cc_final: 0.7889 (p0) REVERT: B 663 ASP cc_start: 0.8152 (p0) cc_final: 0.7854 (p0) REVERT: B 666 ASP cc_start: 0.8233 (t0) cc_final: 0.7747 (p0) REVERT: B 678 HIS cc_start: 0.8307 (m170) cc_final: 0.7984 (m170) REVERT: B 694 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8419 (mtpt) REVERT: B 695 LYS cc_start: 0.8668 (tmtt) cc_final: 0.8381 (tptp) REVERT: B 696 CYS cc_start: 0.8854 (t) cc_final: 0.8099 (p) REVERT: B 723 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: B 727 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8650 (tp) REVERT: B 751 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7496 (tp30) REVERT: B 755 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8538 (ttmm) REVERT: B 770 GLU cc_start: 0.8509 (tp30) cc_final: 0.8212 (mm-30) REVERT: C 262 GLU cc_start: 0.8437 (tp30) cc_final: 0.8222 (tm-30) REVERT: C 267 GLN cc_start: 0.8964 (pt0) cc_final: 0.8340 (pt0) REVERT: C 297 ARG cc_start: 0.8355 (tpt170) cc_final: 0.7851 (tpt170) REVERT: C 324 GLU cc_start: 0.7260 (mp0) cc_final: 0.6601 (mp0) REVERT: C 333 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7560 (tp30) REVERT: C 382 LYS cc_start: 0.7451 (mtmt) cc_final: 0.7175 (mtmm) REVERT: C 391 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7557 (mtm-85) REVERT: C 406 ASP cc_start: 0.7615 (t0) cc_final: 0.6945 (m-30) REVERT: C 421 ASP cc_start: 0.8545 (t0) cc_final: 0.7947 (t0) REVERT: C 425 LYS cc_start: 0.8960 (mttp) cc_final: 0.8634 (mttp) REVERT: C 426 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8496 (mm-40) REVERT: C 453 VAL cc_start: 0.8688 (p) cc_final: 0.8438 (m) REVERT: C 484 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8158 (mm) REVERT: C 488 LEU cc_start: 0.7843 (tp) cc_final: 0.7105 (tp) REVERT: C 490 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7931 (t0) REVERT: C 492 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: C 493 SER cc_start: 0.8934 (t) cc_final: 0.8673 (p) REVERT: C 495 MET cc_start: 0.8718 (ttp) cc_final: 0.8460 (ttm) REVERT: C 497 ASP cc_start: 0.8112 (t0) cc_final: 0.7904 (t0) REVERT: C 512 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8031 (mmmt) REVERT: C 522 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8032 (mm-30) REVERT: C 525 LYS cc_start: 0.8688 (tppp) cc_final: 0.8346 (tppp) REVERT: C 540 GLU cc_start: 0.7990 (pp20) cc_final: 0.7630 (pp20) REVERT: C 563 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8361 (mtmt) REVERT: C 582 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8446 (mmmm) REVERT: C 595 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8013 (mt-10) REVERT: C 599 ARG cc_start: 0.8715 (mtt-85) cc_final: 0.8331 (mtt-85) REVERT: C 600 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: C 645 ASP cc_start: 0.8275 (t0) cc_final: 0.8054 (t0) REVERT: C 676 ASP cc_start: 0.8531 (p0) cc_final: 0.8227 (p0) REVERT: C 685 ASP cc_start: 0.8134 (p0) cc_final: 0.7911 (p0) REVERT: C 691 GLU cc_start: 0.8562 (tp30) cc_final: 0.8010 (tp30) REVERT: C 730 GLU cc_start: 0.8465 (tp30) cc_final: 0.7707 (mm-30) REVERT: C 751 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 755 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8203 (tmtt) REVERT: C 771 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7441 (pp20) REVERT: D 252 LYS cc_start: 0.8552 (tppp) cc_final: 0.8071 (tppp) REVERT: D 280 ARG cc_start: 0.7981 (mpt180) cc_final: 0.7576 (mpt-90) REVERT: D 324 GLU cc_start: 0.7764 (mp0) cc_final: 0.6715 (mp0) REVERT: D 328 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8187 (ttm110) REVERT: D 333 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7282 (tm-30) REVERT: D 374 MET cc_start: 0.8321 (tpt) cc_final: 0.7912 (tpp) REVERT: D 425 LYS cc_start: 0.8938 (mttm) cc_final: 0.8593 (ttmm) REVERT: D 426 GLN cc_start: 0.9012 (tp40) cc_final: 0.8566 (tp40) REVERT: D 428 SER cc_start: 0.9085 (m) cc_final: 0.8790 (p) REVERT: D 434 ARG cc_start: 0.7522 (mtt90) cc_final: 0.7233 (mtt90) REVERT: D 443 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8410 (mmtp) REVERT: D 444 TYR cc_start: 0.8672 (t80) cc_final: 0.8156 (t80) REVERT: D 461 CYS cc_start: 0.8661 (m) cc_final: 0.8294 (t) REVERT: D 463 GLU cc_start: 0.8728 (tp30) cc_final: 0.8489 (tp30) REVERT: D 488 LEU cc_start: 0.8001 (tp) cc_final: 0.7620 (tt) REVERT: D 490 ASP cc_start: 0.8187 (t0) cc_final: 0.7874 (t0) REVERT: D 492 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: D 512 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8029 (ttmm) REVERT: D 513 VAL cc_start: 0.8412 (m) cc_final: 0.8132 (p) REVERT: D 523 GLU cc_start: 0.8146 (tp30) cc_final: 0.7133 (tp30) REVERT: D 525 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8672 (mmmm) REVERT: D 527 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8162 (ttmm) REVERT: D 537 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: D 563 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8151 (mtpt) REVERT: D 600 GLU cc_start: 0.8240 (pp20) cc_final: 0.7792 (pp20) REVERT: D 604 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8494 (ttmt) REVERT: D 642 ASN cc_start: 0.8735 (t0) cc_final: 0.8346 (t0) REVERT: D 661 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6604 (tpt170) REVERT: D 675 LEU cc_start: 0.8656 (tp) cc_final: 0.8433 (mp) REVERT: D 717 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8145 (tm-30) REVERT: D 723 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: D 730 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8173 (mm-30) REVERT: D 751 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7652 (tm-30) REVERT: D 755 LYS cc_start: 0.8749 (tttt) cc_final: 0.8331 (tptp) REVERT: E 242 LEU cc_start: 0.8779 (mm) cc_final: 0.8526 (tp) REVERT: E 262 GLU cc_start: 0.8494 (tp30) cc_final: 0.8289 (tm-30) REVERT: E 297 ARG cc_start: 0.8688 (tpt90) cc_final: 0.8299 (tpt90) REVERT: E 301 ASN cc_start: 0.8830 (t0) cc_final: 0.8575 (t0) REVERT: E 311 ASN cc_start: 0.7833 (m-40) cc_final: 0.7615 (t0) REVERT: E 382 LYS cc_start: 0.7449 (mtpt) cc_final: 0.7137 (mtpt) REVERT: E 401 ARG cc_start: 0.7994 (mmp80) cc_final: 0.7439 (tpp80) REVERT: E 410 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: E 443 LYS cc_start: 0.8957 (tppt) cc_final: 0.8493 (tppt) REVERT: E 444 TYR cc_start: 0.8770 (t80) cc_final: 0.8406 (t80) REVERT: E 461 CYS cc_start: 0.8778 (m) cc_final: 0.8459 (t) REVERT: E 466 MET cc_start: 0.8747 (tpp) cc_final: 0.8540 (tpp) REVERT: E 490 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7925 (t0) REVERT: E 512 LYS cc_start: 0.8447 (ttpt) cc_final: 0.7840 (ttpt) REVERT: E 600 GLU cc_start: 0.8322 (pp20) cc_final: 0.7824 (pp20) REVERT: E 617 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7802 (mp0) REVERT: E 619 ASP cc_start: 0.8574 (m-30) cc_final: 0.8134 (m-30) REVERT: E 642 ASN cc_start: 0.8665 (t0) cc_final: 0.8368 (t0) REVERT: E 661 ARG cc_start: 0.6906 (tpt90) cc_final: 0.6091 (tpt170) REVERT: E 664 GLU cc_start: 0.8500 (tt0) cc_final: 0.8142 (tt0) REVERT: E 666 ASP cc_start: 0.8450 (t0) cc_final: 0.7696 (p0) REVERT: E 678 HIS cc_start: 0.8211 (m170) cc_final: 0.7812 (m170) REVERT: E 694 LYS cc_start: 0.8894 (mttt) cc_final: 0.8492 (mtpt) REVERT: E 696 CYS cc_start: 0.8738 (t) cc_final: 0.8422 (t) REVERT: E 715 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8165 (ttp80) REVERT: E 745 VAL cc_start: 0.8560 (t) cc_final: 0.8088 (m) REVERT: E 752 LYS cc_start: 0.8834 (tmtt) cc_final: 0.8474 (ttmm) REVERT: E 755 LYS cc_start: 0.8710 (tptm) cc_final: 0.8331 (tptm) REVERT: E 770 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8309 (mm-30) REVERT: E 771 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7799 (tm-30) REVERT: F 253 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: F 255 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8122 (tm-30) REVERT: F 261 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8919 (tp) REVERT: F 267 GLN cc_start: 0.8823 (pt0) cc_final: 0.8577 (pt0) REVERT: F 274 PHE cc_start: 0.9030 (m-80) cc_final: 0.8789 (m-10) REVERT: F 285 HIS cc_start: 0.7946 (m-70) cc_final: 0.7363 (m-70) REVERT: F 311 ASN cc_start: 0.7968 (t0) cc_final: 0.7628 (t0) REVERT: F 333 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7665 (tp30) REVERT: F 335 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8292 (mtp-110) REVERT: F 346 GLU cc_start: 0.7766 (mp0) cc_final: 0.7545 (mp0) REVERT: F 374 MET cc_start: 0.7848 (tpt) cc_final: 0.7569 (tpt) REVERT: F 391 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7681 (mtm-85) REVERT: F 406 ASP cc_start: 0.7382 (t0) cc_final: 0.6655 (m-30) REVERT: F 443 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8541 (mmtt) REVERT: F 444 TYR cc_start: 0.8829 (t80) cc_final: 0.8115 (t80) REVERT: F 468 THR cc_start: 0.8545 (m) cc_final: 0.8021 (p) REVERT: F 488 LEU cc_start: 0.7662 (tp) cc_final: 0.7206 (tt) REVERT: F 490 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8061 (t0) REVERT: F 513 VAL cc_start: 0.8791 (m) cc_final: 0.8537 (p) REVERT: F 536 LEU cc_start: 0.9049 (mm) cc_final: 0.8674 (tp) REVERT: F 540 GLU cc_start: 0.7971 (pp20) cc_final: 0.7636 (pp20) REVERT: F 573 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7775 (mp0) REVERT: F 621 LEU cc_start: 0.7797 (mt) cc_final: 0.7528 (mp) REVERT: F 642 ASN cc_start: 0.8401 (t0) cc_final: 0.8134 (t0) REVERT: F 691 GLU cc_start: 0.8504 (tp30) cc_final: 0.7736 (tp30) REVERT: F 699 LYS cc_start: 0.9024 (tptp) cc_final: 0.8791 (tppt) REVERT: F 723 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: F 729 GLN cc_start: 0.8554 (mt0) cc_final: 0.8236 (mt0) REVERT: F 746 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7654 (mp0) REVERT: F 751 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7560 (tm-30) REVERT: F 754 PHE cc_start: 0.8578 (t80) cc_final: 0.8335 (t80) REVERT: F 755 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8347 (ttmm) outliers start: 111 outliers final: 70 residues processed: 929 average time/residue: 0.1974 time to fit residues: 266.3374 Evaluate side-chains 972 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 872 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 443 LYS Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 301 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 738 GLU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 600 GLU Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 723 GLU Chi-restraints excluded: chain F residue 774 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 5 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN C 710 HIS ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.133449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110912 restraints weight = 44478.535| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.52 r_work: 0.3298 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25790 Z= 0.191 Angle : 0.724 10.076 34986 Z= 0.355 Chirality : 0.046 0.176 4020 Planarity : 0.006 0.098 4488 Dihedral : 12.033 159.969 3816 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.74 % Allowed : 23.93 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 3240 helix: 1.07 (0.13), residues: 1620 sheet: 0.55 (0.29), residues: 348 loop : -0.12 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 775 TYR 0.043 0.001 TYR C 444 PHE 0.030 0.002 PHE B 754 TRP 0.020 0.002 TRP E 515 HIS 0.012 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00430 (25782) covalent geometry : angle 0.72438 (34986) hydrogen bonds : bond 0.03668 ( 1230) hydrogen bonds : angle 4.16752 ( 3498) Misc. bond : bond 0.00084 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 893 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.8289 (tp30) cc_final: 0.7829 (tm-30) REVERT: A 253 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: A 255 GLU cc_start: 0.8773 (tt0) cc_final: 0.8412 (tm-30) REVERT: A 297 ARG cc_start: 0.8802 (tpt170) cc_final: 0.8452 (tpt170) REVERT: A 324 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: A 328 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8394 (ttm110) REVERT: A 333 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 335 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8412 (mtp-110) REVERT: A 406 ASP cc_start: 0.7886 (t0) cc_final: 0.7177 (m-30) REVERT: A 426 GLN cc_start: 0.8993 (tp40) cc_final: 0.8776 (mm-40) REVERT: A 443 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8680 (tppt) REVERT: A 444 TYR cc_start: 0.8698 (t80) cc_final: 0.8327 (t80) REVERT: A 448 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8278 (mttt) REVERT: A 453 VAL cc_start: 0.8969 (p) cc_final: 0.8582 (m) REVERT: A 485 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8218 (mmtp) REVERT: A 487 THR cc_start: 0.8949 (t) cc_final: 0.8535 (p) REVERT: A 488 LEU cc_start: 0.8181 (tp) cc_final: 0.7652 (tp) REVERT: A 490 ASP cc_start: 0.8370 (t0) cc_final: 0.7941 (t0) REVERT: A 492 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: A 512 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8123 (tttm) REVERT: A 514 TYR cc_start: 0.8679 (m-10) cc_final: 0.8093 (m-10) REVERT: A 523 GLU cc_start: 0.8279 (tp30) cc_final: 0.7552 (tp30) REVERT: A 540 GLU cc_start: 0.7941 (pp20) cc_final: 0.7515 (pp20) REVERT: A 548 SER cc_start: 0.8834 (m) cc_final: 0.8357 (p) REVERT: A 556 TYR cc_start: 0.8456 (p90) cc_final: 0.8075 (p90) REVERT: A 582 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8583 (mmmm) REVERT: A 585 GLU cc_start: 0.8023 (pt0) cc_final: 0.7542 (pp20) REVERT: A 586 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8231 (tp) REVERT: A 595 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8101 (mm-30) REVERT: A 600 GLU cc_start: 0.8296 (pp20) cc_final: 0.7798 (pp20) REVERT: A 651 LYS cc_start: 0.8945 (tppt) cc_final: 0.8676 (tppt) REVERT: A 661 ARG cc_start: 0.7842 (mmm160) cc_final: 0.7084 (mmm160) REVERT: A 663 ASP cc_start: 0.7786 (p0) cc_final: 0.6769 (p0) REVERT: A 695 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8568 (tptp) REVERT: A 717 GLU cc_start: 0.8428 (tp30) cc_final: 0.8075 (tp30) REVERT: A 737 MET cc_start: 0.7626 (ttm) cc_final: 0.7397 (ttm) REVERT: A 751 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7330 (tp30) REVERT: A 752 LYS cc_start: 0.8980 (tttm) cc_final: 0.8625 (ttmm) REVERT: A 755 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8537 (ttmt) REVERT: A 764 GLU cc_start: 0.7965 (mp0) cc_final: 0.7629 (mp0) REVERT: B 262 GLU cc_start: 0.8512 (tp30) cc_final: 0.8298 (tp30) REVERT: B 297 ARG cc_start: 0.8808 (tpt170) cc_final: 0.8489 (tpt170) REVERT: B 301 ASN cc_start: 0.8861 (t0) cc_final: 0.8545 (t0) REVERT: B 311 ASN cc_start: 0.7954 (t0) cc_final: 0.7617 (t0) REVERT: B 324 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: B 328 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8309 (ttm110) REVERT: B 333 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 346 GLU cc_start: 0.7618 (mp0) cc_final: 0.7343 (mp0) REVERT: B 391 ARG cc_start: 0.8324 (ptt-90) cc_final: 0.7685 (ptt-90) REVERT: B 421 ASP cc_start: 0.8807 (t0) cc_final: 0.8395 (t0) REVERT: B 448 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8092 (mtmt) REVERT: B 461 CYS cc_start: 0.8810 (t) cc_final: 0.8583 (t) REVERT: B 463 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 468 THR cc_start: 0.8722 (m) cc_final: 0.8140 (p) REVERT: B 484 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8365 (mm) REVERT: B 490 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8076 (t0) REVERT: B 492 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: B 493 SER cc_start: 0.9033 (t) cc_final: 0.8665 (p) REVERT: B 497 ASP cc_start: 0.8193 (t0) cc_final: 0.7797 (t0) REVERT: B 512 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7842 (ttpp) REVERT: B 525 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8347 (mmtp) REVERT: B 534 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8659 (tp) REVERT: B 540 GLU cc_start: 0.8002 (pp20) cc_final: 0.7722 (pp20) REVERT: B 556 TYR cc_start: 0.8397 (p90) cc_final: 0.8036 (p90) REVERT: B 582 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8481 (mtmm) REVERT: B 585 GLU cc_start: 0.8328 (pt0) cc_final: 0.7585 (pp20) REVERT: B 587 PHE cc_start: 0.7905 (t80) cc_final: 0.7530 (t80) REVERT: B 600 GLU cc_start: 0.8342 (pp20) cc_final: 0.7793 (pp20) REVERT: B 617 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7958 (mm-30) REVERT: B 638 THR cc_start: 0.8716 (t) cc_final: 0.8383 (p) REVERT: B 642 ASN cc_start: 0.8607 (t0) cc_final: 0.8298 (t0) REVERT: B 643 GLU cc_start: 0.8694 (tp30) cc_final: 0.8177 (tp30) REVERT: B 660 ASN cc_start: 0.8729 (p0) cc_final: 0.7941 (p0) REVERT: B 663 ASP cc_start: 0.8185 (p0) cc_final: 0.7928 (p0) REVERT: B 666 ASP cc_start: 0.8269 (t0) cc_final: 0.7804 (p0) REVERT: B 678 HIS cc_start: 0.8267 (m170) cc_final: 0.7959 (m170) REVERT: B 694 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8433 (mtpt) REVERT: B 695 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8391 (tptp) REVERT: B 696 CYS cc_start: 0.8856 (t) cc_final: 0.8095 (p) REVERT: B 723 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: B 727 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8690 (tp) REVERT: B 751 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7574 (tp30) REVERT: B 755 LYS cc_start: 0.8854 (ttmm) cc_final: 0.8581 (ttmm) REVERT: B 770 GLU cc_start: 0.8567 (tp30) cc_final: 0.8269 (mm-30) REVERT: C 255 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8122 (tm-30) REVERT: C 267 GLN cc_start: 0.8955 (pt0) cc_final: 0.8596 (pt0) REVERT: C 297 ARG cc_start: 0.8416 (tpt170) cc_final: 0.7955 (tpt170) REVERT: C 333 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7599 (tp30) REVERT: C 382 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7205 (mtmm) REVERT: C 391 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7543 (mtm-85) REVERT: C 401 ARG cc_start: 0.8196 (tpp-160) cc_final: 0.7945 (tpp-160) REVERT: C 406 ASP cc_start: 0.7755 (t0) cc_final: 0.7059 (m-30) REVERT: C 421 ASP cc_start: 0.8523 (t0) cc_final: 0.7966 (t0) REVERT: C 425 LYS cc_start: 0.8951 (mttp) cc_final: 0.8653 (mttp) REVERT: C 426 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8587 (mm-40) REVERT: C 453 VAL cc_start: 0.8870 (p) cc_final: 0.8598 (m) REVERT: C 484 LEU cc_start: 0.8548 (mm) cc_final: 0.8211 (mm) REVERT: C 488 LEU cc_start: 0.7927 (tp) cc_final: 0.7199 (tp) REVERT: C 490 ASP cc_start: 0.8385 (t0) cc_final: 0.7974 (t0) REVERT: C 492 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: C 493 SER cc_start: 0.8961 (t) cc_final: 0.8597 (p) REVERT: C 495 MET cc_start: 0.8726 (ttp) cc_final: 0.8510 (ttm) REVERT: C 512 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8057 (mmmt) REVERT: C 522 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8065 (mm-30) REVERT: C 525 LYS cc_start: 0.8697 (tppp) cc_final: 0.8336 (tppp) REVERT: C 540 GLU cc_start: 0.8021 (pp20) cc_final: 0.7657 (pp20) REVERT: C 582 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8460 (mmmm) REVERT: C 595 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 599 ARG cc_start: 0.8772 (mtt-85) cc_final: 0.8392 (mtt-85) REVERT: C 600 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: C 645 ASP cc_start: 0.8298 (t0) cc_final: 0.8082 (t0) REVERT: C 676 ASP cc_start: 0.8566 (p0) cc_final: 0.7971 (p0) REVERT: C 685 ASP cc_start: 0.8136 (p0) cc_final: 0.7916 (p0) REVERT: C 691 GLU cc_start: 0.8568 (tp30) cc_final: 0.8026 (tp30) REVERT: C 712 LEU cc_start: 0.8849 (mt) cc_final: 0.8541 (mm) REVERT: C 715 ARG cc_start: 0.8553 (ttp-170) cc_final: 0.8269 (ptm160) REVERT: C 730 GLU cc_start: 0.8461 (tp30) cc_final: 0.8002 (mm-30) REVERT: C 751 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7769 (tm-30) REVERT: C 755 LYS cc_start: 0.8629 (tmtt) cc_final: 0.8247 (tmtt) REVERT: C 771 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7458 (pp20) REVERT: D 240 GLU cc_start: 0.8376 (tp30) cc_final: 0.7799 (tm-30) REVERT: D 252 LYS cc_start: 0.8575 (tppp) cc_final: 0.8117 (tppp) REVERT: D 280 ARG cc_start: 0.8045 (mpt180) cc_final: 0.7633 (mpt-90) REVERT: D 328 ARG cc_start: 0.8769 (ttm110) cc_final: 0.8209 (ttm110) REVERT: D 333 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7327 (tm-30) REVERT: D 374 MET cc_start: 0.8339 (tpt) cc_final: 0.7948 (tpp) REVERT: D 425 LYS cc_start: 0.8988 (mttm) cc_final: 0.8629 (ttmm) REVERT: D 428 SER cc_start: 0.9106 (m) cc_final: 0.8822 (p) REVERT: D 434 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7344 (mtt90) REVERT: D 443 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8448 (mmtp) REVERT: D 444 TYR cc_start: 0.8745 (t80) cc_final: 0.8181 (t80) REVERT: D 461 CYS cc_start: 0.8659 (m) cc_final: 0.8320 (t) REVERT: D 463 GLU cc_start: 0.8733 (tp30) cc_final: 0.8472 (tp30) REVERT: D 485 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7858 (mmtt) REVERT: D 488 LEU cc_start: 0.7987 (tp) cc_final: 0.7604 (tt) REVERT: D 490 ASP cc_start: 0.8218 (t0) cc_final: 0.7905 (t0) REVERT: D 492 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: D 512 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8055 (ttmm) REVERT: D 513 VAL cc_start: 0.8428 (m) cc_final: 0.8012 (p) REVERT: D 517 ASP cc_start: 0.8804 (m-30) cc_final: 0.8233 (m-30) REVERT: D 523 GLU cc_start: 0.8152 (tp30) cc_final: 0.7145 (tp30) REVERT: D 525 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8678 (mmmm) REVERT: D 527 LYS cc_start: 0.8896 (mtpp) cc_final: 0.8182 (ttmm) REVERT: D 537 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: D 600 GLU cc_start: 0.8296 (pp20) cc_final: 0.7870 (pp20) REVERT: D 604 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8447 (ttpt) REVERT: D 642 ASN cc_start: 0.8737 (t0) cc_final: 0.8350 (t0) REVERT: D 675 LEU cc_start: 0.8729 (tp) cc_final: 0.8389 (mt) REVERT: D 717 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8175 (tm-30) REVERT: D 723 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: D 730 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8053 (mm-30) REVERT: D 751 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7634 (tm-30) REVERT: D 752 LYS cc_start: 0.8828 (tptp) cc_final: 0.8360 (tptp) REVERT: D 755 LYS cc_start: 0.8766 (tttt) cc_final: 0.8341 (tptp) REVERT: D 771 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7868 (pp20) REVERT: E 242 LEU cc_start: 0.8759 (mm) cc_final: 0.8506 (tp) REVERT: E 297 ARG cc_start: 0.8719 (tpt90) cc_final: 0.8343 (tpt90) REVERT: E 301 ASN cc_start: 0.8859 (t0) cc_final: 0.8572 (t0) REVERT: E 311 ASN cc_start: 0.7838 (m-40) cc_final: 0.7623 (t0) REVERT: E 382 LYS cc_start: 0.7469 (mtpt) cc_final: 0.7139 (mtpt) REVERT: E 401 ARG cc_start: 0.8104 (mmp80) cc_final: 0.7570 (tpp80) REVERT: E 408 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7637 (tp30) REVERT: E 410 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7683 (mm-30) REVERT: E 443 LYS cc_start: 0.8992 (tppt) cc_final: 0.8552 (tppt) REVERT: E 444 TYR cc_start: 0.8765 (t80) cc_final: 0.8536 (t80) REVERT: E 461 CYS cc_start: 0.8808 (m) cc_final: 0.8499 (t) REVERT: E 466 MET cc_start: 0.8805 (tpp) cc_final: 0.8578 (tpp) REVERT: E 490 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8107 (t0) REVERT: E 600 GLU cc_start: 0.8370 (pp20) cc_final: 0.7884 (pp20) REVERT: E 638 THR cc_start: 0.8735 (t) cc_final: 0.8405 (p) REVERT: E 642 ASN cc_start: 0.8686 (t0) cc_final: 0.8424 (t0) REVERT: E 661 ARG cc_start: 0.6927 (tpt90) cc_final: 0.6480 (tpt170) REVERT: E 664 GLU cc_start: 0.8483 (tt0) cc_final: 0.8224 (tt0) REVERT: E 666 ASP cc_start: 0.8486 (t0) cc_final: 0.7747 (p0) REVERT: E 676 ASP cc_start: 0.8512 (p0) cc_final: 0.8258 (p0) REVERT: E 678 HIS cc_start: 0.8228 (m170) cc_final: 0.7907 (m170) REVERT: E 694 LYS cc_start: 0.8884 (mttt) cc_final: 0.8386 (mtpt) REVERT: E 696 CYS cc_start: 0.8711 (t) cc_final: 0.8395 (t) REVERT: E 745 VAL cc_start: 0.8572 (t) cc_final: 0.8120 (m) REVERT: E 751 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7535 (tp30) REVERT: E 752 LYS cc_start: 0.8836 (tmtt) cc_final: 0.8475 (ttmm) REVERT: E 755 LYS cc_start: 0.8726 (tptm) cc_final: 0.8237 (tptm) REVERT: E 770 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8309 (mm-30) REVERT: E 771 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7828 (tm-30) REVERT: F 255 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8166 (tm-30) REVERT: F 261 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8926 (tp) REVERT: F 274 PHE cc_start: 0.9061 (m-80) cc_final: 0.8819 (m-10) REVERT: F 285 HIS cc_start: 0.7935 (m-70) cc_final: 0.7311 (m-70) REVERT: F 311 ASN cc_start: 0.7993 (t0) cc_final: 0.7622 (t0) REVERT: F 333 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7722 (tp30) REVERT: F 335 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8329 (mtp-110) REVERT: F 346 GLU cc_start: 0.7805 (mp0) cc_final: 0.7552 (mp0) REVERT: F 374 MET cc_start: 0.7834 (tpt) cc_final: 0.7630 (tpt) REVERT: F 391 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7699 (mtm-85) REVERT: F 406 ASP cc_start: 0.7549 (t0) cc_final: 0.6810 (m-30) REVERT: F 443 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8642 (mmtt) REVERT: F 444 TYR cc_start: 0.8834 (t80) cc_final: 0.8064 (t80) REVERT: F 468 THR cc_start: 0.8532 (m) cc_final: 0.8004 (p) REVERT: F 488 LEU cc_start: 0.7714 (tp) cc_final: 0.7243 (tt) REVERT: F 490 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8103 (t0) REVERT: F 512 LYS cc_start: 0.8572 (tppp) cc_final: 0.8266 (tppp) REVERT: F 513 VAL cc_start: 0.8744 (m) cc_final: 0.8463 (p) REVERT: F 522 GLU cc_start: 0.8398 (tp30) cc_final: 0.8159 (mm-30) REVERT: F 525 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8550 (mttt) REVERT: F 536 LEU cc_start: 0.9062 (mm) cc_final: 0.8689 (tp) REVERT: F 540 GLU cc_start: 0.8003 (pp20) cc_final: 0.7682 (pp20) REVERT: F 563 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8378 (mtpp) REVERT: F 572 THR cc_start: 0.8630 (m) cc_final: 0.8243 (p) REVERT: F 573 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7663 (mm-30) REVERT: F 642 ASN cc_start: 0.8425 (t0) cc_final: 0.8163 (t0) REVERT: F 661 ARG cc_start: 0.7139 (tpt170) cc_final: 0.6650 (tpt170) REVERT: F 664 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7890 (tm-30) REVERT: F 691 GLU cc_start: 0.8566 (tp30) cc_final: 0.7770 (tp30) REVERT: F 699 LYS cc_start: 0.9017 (tptp) cc_final: 0.8763 (tppt) REVERT: F 723 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: F 729 GLN cc_start: 0.8593 (mt0) cc_final: 0.8280 (mt0) REVERT: F 746 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7683 (mp0) REVERT: F 751 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7611 (tm-30) REVERT: F 754 PHE cc_start: 0.8664 (t80) cc_final: 0.8420 (t80) REVERT: F 755 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8344 (ttmm) outliers start: 101 outliers final: 61 residues processed: 937 average time/residue: 0.1980 time to fit residues: 268.9058 Evaluate side-chains 958 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 870 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 301 ASN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 434 ARG Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 636 VAL Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 723 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 6 optimal weight: 0.4980 chunk 294 optimal weight: 1.9990 chunk 119 optimal weight: 0.0670 chunk 280 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 205 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN C 304 ASN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.136355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113720 restraints weight = 44322.088| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.54 r_work: 0.3348 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25790 Z= 0.130 Angle : 0.708 10.564 34986 Z= 0.343 Chirality : 0.044 0.243 4020 Planarity : 0.005 0.088 4488 Dihedral : 11.752 161.712 3816 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.44 % Allowed : 24.56 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 3240 helix: 1.19 (0.13), residues: 1596 sheet: 0.56 (0.29), residues: 348 loop : -0.04 (0.20), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 775 TYR 0.040 0.001 TYR C 444 PHE 0.031 0.002 PHE B 754 TRP 0.017 0.002 TRP E 515 HIS 0.010 0.001 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00303 (25782) covalent geometry : angle 0.70817 (34986) hydrogen bonds : bond 0.03430 ( 1230) hydrogen bonds : angle 4.09780 ( 3498) Misc. bond : bond 0.00091 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5981.40 seconds wall clock time: 103 minutes 10.21 seconds (6190.21 seconds total)