Starting phenix.real_space_refine on Fri Aug 9 06:31:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/08_2024/7nku_12448.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/08_2024/7nku_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/08_2024/7nku_12448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/08_2024/7nku_12448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/08_2024/7nku_12448.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nku_12448/08_2024/7nku_12448.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 676": "OD1" <-> "OD2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 456": "OD1" <-> "OD2" Residue "B ASP 517": "OD1" <-> "OD2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 708": "OD1" <-> "OD2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 345": "OD1" <-> "OD2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C GLU 522": "OE1" <-> "OE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 708": "OD1" <-> "OD2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ASP 396": "OD1" <-> "OD2" Residue "D PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 421": "OD1" <-> "OD2" Residue "D ASP 433": "OD1" <-> "OD2" Residue "D ASP 456": "OD1" <-> "OD2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ASP 421": "OD1" <-> "OD2" Residue "E ASP 433": "OD1" <-> "OD2" Residue "E GLU 522": "OE1" <-> "OE2" Residue "E TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 708": "OD1" <-> "OD2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F ASP 421": "OD1" <-> "OD2" Residue "F ASP 433": "OD1" <-> "OD2" Residue "F ASP 517": "OD1" <-> "OD2" Residue "F ASP 663": "OD1" <-> "OD2" Residue "F PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 708": "OD1" <-> "OD2" Residue "F GLU 738": "OE1" <-> "OE2" Residue "F ASP 741": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 14.21, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 10.59 Conformation dependent library (CDL) restraints added in 4.4 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: 3.06 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: 9.25 Time building geometry restraints manager: 11.45 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: 88.75 - 97.84: 7 97.84 - 106.93: 974 106.93 - 116.02: 16327 116.02 - 125.11: 17317 125.11 - 134.20: 361 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: 0.00 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: 1.780 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: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 69.780 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.630 ------------------------------------------------------------------------------- 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 25782 Z= 0.502 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 : 17.36 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP F 515 HIS 0.011 0.001 HIS B 306 PHE 0.024 0.002 PHE D 700 TYR 0.053 0.002 TYR C 444 ARG 0.018 0.001 ARG F 328 *********************** 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 fitting. rotamer outliers: 0 poor density : 1040 time to evaluate : 2.624 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: 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: 0.6676 (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: 0.7964 (t80) REVERT: A 448 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7853 (mttt) 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: 0.7965 (tp) REVERT: A 489 LYS cc_start: 0.8420 (mppt) cc_final: 0.8033 (mppt) REVERT: A 492 GLU cc_start: 0.7734 (mp0) cc_final: 0.7340 (mp0) REVERT: A 499 ARG cc_start: 0.6922 (tpm170) cc_final: 0.4573 (tpp-160) REVERT: A 513 VAL cc_start: 0.8820 (m) cc_final: 0.8345 (p) REVERT: A 514 TYR cc_start: 0.8541 (m-10) cc_final: 0.8114 (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: 0.8177 (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: 0.8196 (p) REVERT: A 582 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8065 (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: 0.7108 (p0) REVERT: A 664 GLU cc_start: 0.7850 (pt0) cc_final: 0.7506 (pt0) REVERT: A 691 GLU cc_start: 0.8195 (tp30) cc_final: 0.7547 (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: 0.8312 (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: 0.7240 (tm-30) REVERT: A 730 GLU cc_start: 0.7769 (tp30) cc_final: 0.7562 (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: 0.8025 (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: 0.6611 (tm-30) REVERT: B 335 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7727 (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: 0.8158 (t80) REVERT: B 463 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 485 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8138 (mmtp) REVERT: B 488 LEU cc_start: 0.8494 (tp) cc_final: 0.8079 (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: 0.8601 (p) REVERT: B 497 ASP cc_start: 0.7478 (t0) cc_final: 0.7053 (t0) REVERT: B 514 TYR cc_start: 0.8794 (m-10) cc_final: 0.8542 (m-80) REVERT: B 530 GLU cc_start: 0.7904 (tt0) cc_final: 0.7143 (tt0) REVERT: B 540 GLU cc_start: 0.7540 (pp20) cc_final: 0.7332 (pp20) REVERT: B 572 THR cc_start: 0.8371 (m) cc_final: 0.8137 (m) 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: 0.8052 (t0) REVERT: B 643 GLU cc_start: 0.7902 (tp30) cc_final: 0.7614 (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: 0.7584 (pt0) REVERT: B 680 TYR cc_start: 0.8686 (t80) cc_final: 0.8364 (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: 0.8356 (tptp) REVERT: B 696 CYS cc_start: 0.8061 (t) cc_final: 0.7800 (t) REVERT: B 715 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7555 (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: 0.6904 (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: 0.8414 (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: 0.7619 (tp30) REVERT: C 292 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8640 (mttp) REVERT: C 308 LEU cc_start: 0.8780 (mp) cc_final: 0.8304 (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: 0.6884 (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: 0.8150 (m-40) REVERT: C 426 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8106 (mm-40) REVERT: C 443 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8489 (mmtp) REVERT: C 453 VAL cc_start: 0.9075 (p) cc_final: 0.8745 (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: 0.8032 (p) REVERT: C 493 SER cc_start: 0.8845 (t) cc_final: 0.8314 (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: 0.7970 (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: 0.8030 (tppp) REVERT: C 540 GLU cc_start: 0.7551 (pp20) cc_final: 0.7283 (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: 0.7804 (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: 0.7887 (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: 0.7344 (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: 0.6970 (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: 0.8540 (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: 0.8409 (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: 0.8285 (mp) REVERT: D 328 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8044 (ttm110) REVERT: D 333 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6432 (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: 0.8457 (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: 0.7564 (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: 0.8349 (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: 0.7855 (ttp-170) REVERT: D 717 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 723 GLU cc_start: 0.7449 (mp0) cc_final: 0.6880 (mp0) REVERT: D 751 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7249 (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: 0.7190 (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: 0.8000 (ttpt) REVERT: E 463 GLU cc_start: 0.8374 (tp30) cc_final: 0.8152 (tp30) REVERT: E 484 LEU cc_start: 0.7891 (mp) cc_final: 0.7610 (tp) REVERT: E 488 LEU cc_start: 0.8755 (tt) cc_final: 0.7928 (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: 0.8121 (mm) REVERT: E 600 GLU cc_start: 0.7817 (pp20) cc_final: 0.7345 (pp20) REVERT: E 619 ASP cc_start: 0.7938 (m-30) cc_final: 0.7458 (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: 0.8375 (tptp) REVERT: E 696 CYS cc_start: 0.8074 (t) cc_final: 0.7796 (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: 0.7705 (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: 0.7559 (tm-30) REVERT: F 308 LEU cc_start: 0.8517 (mp) cc_final: 0.8240 (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: 0.8180 (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: 0.7934 (mmtt) REVERT: F 488 LEU cc_start: 0.8071 (tt) cc_final: 0.7702 (tt) REVERT: F 489 LYS cc_start: 0.8113 (mppt) cc_final: 0.7892 (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: 0.6561 (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: 0.8482 (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: 0.6451 (tpt170) REVERT: F 663 ASP cc_start: 0.8284 (p0) cc_final: 0.7963 (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: 0.8553 (t0) REVERT: F 691 GLU cc_start: 0.8205 (tp30) cc_final: 0.7797 (tp30) REVERT: F 729 GLN cc_start: 0.8541 (mt0) cc_final: 0.8236 (mt0) REVERT: F 730 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7670 (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: 0.8376 (t80) REVERT: F 770 GLU cc_start: 0.7541 (tp30) cc_final: 0.6991 (tp30) outliers start: 0 outliers final: 0 residues processed: 1040 average time/residue: 0.4484 time to fit residues: 672.9046 Evaluate side-chains 954 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 294 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25782 Z= 0.264 Angle : 0.738 13.253 34986 Z= 0.371 Chirality : 0.047 0.266 4020 Planarity : 0.007 0.114 4488 Dihedral : 13.478 154.752 3816 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.70 % Allowed : 13.04 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3240 helix: 0.66 (0.13), residues: 1548 sheet: 0.30 (0.29), residues: 348 loop : -0.65 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 515 HIS 0.005 0.001 HIS D 749 PHE 0.033 0.002 PHE D 587 TYR 0.026 0.002 TYR C 444 ARG 0.010 0.001 ARG F 775 *********************** 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 1046 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1000 time to evaluate : 2.863 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: A 240 GLU cc_start: 0.7681 (tp30) cc_final: 0.7479 (tm-30) REVERT: A 247 VAL cc_start: 0.8869 (t) cc_final: 0.8490 (p) REVERT: A 301 ASN cc_start: 0.7873 (m-40) cc_final: 0.7550 (m-40) REVERT: A 333 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 335 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7720 (mtp-110) REVERT: A 429 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7754 (mmm-85) REVERT: A 430 MET cc_start: 0.8014 (ptp) cc_final: 0.7809 (ptp) REVERT: A 443 LYS cc_start: 0.8723 (mmpt) cc_final: 0.8248 (mmmm) REVERT: A 444 TYR cc_start: 0.8480 (t80) cc_final: 0.8141 (t80) REVERT: A 489 LYS cc_start: 0.8114 (mppt) cc_final: 0.7853 (mppt) REVERT: A 495 MET cc_start: 0.8161 (mtp) cc_final: 0.7918 (ttm) REVERT: A 499 ARG cc_start: 0.6232 (tpm170) cc_final: 0.4148 (mmm160) REVERT: A 512 LYS cc_start: 0.8480 (tttp) cc_final: 0.8184 (tttp) REVERT: A 514 TYR cc_start: 0.8380 (m-10) cc_final: 0.8138 (m-10) REVERT: A 523 GLU cc_start: 0.7409 (tp30) cc_final: 0.6954 (tp30) REVERT: A 530 GLU cc_start: 0.7584 (tt0) cc_final: 0.7364 (tt0) REVERT: A 540 GLU cc_start: 0.7341 (pp20) cc_final: 0.6971 (pp20) REVERT: A 548 SER cc_start: 0.8737 (m) cc_final: 0.8451 (p) REVERT: A 556 TYR cc_start: 0.8163 (p90) cc_final: 0.7903 (p90) REVERT: A 582 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8373 (mmmm) REVERT: A 586 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8637 (tp) REVERT: A 595 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7794 (mp0) REVERT: A 661 ARG cc_start: 0.7200 (mmm160) cc_final: 0.6915 (mmm160) REVERT: A 663 ASP cc_start: 0.7635 (p0) cc_final: 0.7137 (p0) REVERT: A 664 GLU cc_start: 0.7796 (pt0) cc_final: 0.7493 (pt0) REVERT: A 695 LYS cc_start: 0.8596 (tmtt) cc_final: 0.8302 (tptp) REVERT: A 698 LYS cc_start: 0.8934 (ptmm) cc_final: 0.8490 (ptpp) REVERT: A 701 ASN cc_start: 0.7769 (m-40) cc_final: 0.7520 (m-40) REVERT: A 717 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 723 GLU cc_start: 0.7550 (mp0) cc_final: 0.7042 (mp0) REVERT: A 737 MET cc_start: 0.6711 (ttm) cc_final: 0.6429 (ttm) REVERT: A 751 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6941 (tm-30) REVERT: A 752 LYS cc_start: 0.8744 (tttm) cc_final: 0.8383 (ttmm) REVERT: A 755 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8399 (ttmt) REVERT: B 262 GLU cc_start: 0.7921 (tp30) cc_final: 0.7693 (tp30) REVERT: B 328 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7827 (ttm110) REVERT: B 333 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6878 (tm-30) REVERT: B 391 ARG cc_start: 0.7974 (ptt-90) cc_final: 0.7049 (ptt-90) REVERT: B 421 ASP cc_start: 0.8266 (t0) cc_final: 0.7980 (t0) REVERT: B 434 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7495 (mmm-85) REVERT: B 444 TYR cc_start: 0.8433 (t80) cc_final: 0.8173 (t80) REVERT: B 448 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8036 (mtpt) REVERT: B 463 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7652 (mm-30) REVERT: B 486 VAL cc_start: 0.8946 (p) cc_final: 0.8680 (m) REVERT: B 490 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7520 (t0) REVERT: B 493 SER cc_start: 0.8712 (t) cc_final: 0.8509 (p) REVERT: B 497 ASP cc_start: 0.7307 (t0) cc_final: 0.6899 (t0) REVERT: B 525 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8139 (mmtt) REVERT: B 530 GLU cc_start: 0.7951 (tt0) cc_final: 0.7282 (tt0) REVERT: B 540 GLU cc_start: 0.7483 (pp20) cc_final: 0.7262 (pp20) REVERT: B 587 PHE cc_start: 0.7480 (t80) cc_final: 0.7186 (t80) REVERT: B 600 GLU cc_start: 0.7632 (pp20) cc_final: 0.7185 (pp20) REVERT: B 619 ASP cc_start: 0.7912 (m-30) cc_final: 0.7676 (m-30) REVERT: B 638 THR cc_start: 0.8459 (t) cc_final: 0.8070 (p) REVERT: B 641 LEU cc_start: 0.9104 (mt) cc_final: 0.8870 (mm) REVERT: B 642 ASN cc_start: 0.8300 (t0) cc_final: 0.8010 (t0) REVERT: B 643 GLU cc_start: 0.7916 (tp30) cc_final: 0.7681 (tp30) REVERT: B 661 ARG cc_start: 0.7016 (tpt170) cc_final: 0.6335 (tpm170) REVERT: B 677 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7425 (mmt-90) REVERT: B 695 LYS cc_start: 0.8477 (tmtt) cc_final: 0.8254 (tptm) REVERT: B 696 CYS cc_start: 0.7933 (t) cc_final: 0.7683 (t) REVERT: B 717 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7278 (tm-30) REVERT: B 751 GLU cc_start: 0.7669 (tm-30) cc_final: 0.6969 (tm-30) REVERT: B 752 LYS cc_start: 0.8704 (tttm) cc_final: 0.8315 (ttmm) REVERT: B 755 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8385 (ttmm) REVERT: C 252 LYS cc_start: 0.8378 (mttm) cc_final: 0.8166 (mttm) REVERT: C 255 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7385 (tm-30) REVERT: C 262 GLU cc_start: 0.7945 (tp30) cc_final: 0.7680 (tp30) REVERT: C 333 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6809 (tp30) REVERT: C 382 LYS cc_start: 0.7195 (mtmt) cc_final: 0.6885 (mtmm) REVERT: C 391 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7068 (ptt90) REVERT: C 393 ASN cc_start: 0.8368 (m-40) cc_final: 0.8111 (m-40) REVERT: C 406 ASP cc_start: 0.6925 (t0) cc_final: 0.6434 (m-30) REVERT: C 420 PHE cc_start: 0.8872 (t80) cc_final: 0.8660 (t80) REVERT: C 426 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8120 (mm110) REVERT: C 443 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8423 (mmtp) REVERT: C 463 GLU cc_start: 0.8180 (tp30) cc_final: 0.7954 (tp30) REVERT: C 467 LYS cc_start: 0.8554 (mttm) cc_final: 0.8325 (mmtp) REVERT: C 490 ASP cc_start: 0.8067 (t0) cc_final: 0.7384 (t0) REVERT: C 493 SER cc_start: 0.8785 (t) cc_final: 0.8254 (p) REVERT: C 512 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7963 (mmmt) REVERT: C 522 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7427 (mm-30) REVERT: C 525 LYS cc_start: 0.8291 (tppp) cc_final: 0.8086 (tppp) REVERT: C 582 LYS cc_start: 0.8551 (mmmm) cc_final: 0.8293 (mmmm) REVERT: C 595 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7830 (mt-10) REVERT: C 599 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7657 (ttm-80) REVERT: C 600 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: C 661 ARG cc_start: 0.7093 (tpt170) cc_final: 0.6547 (tpt170) REVERT: C 671 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.7849 (ttm-80) REVERT: C 708 ASP cc_start: 0.8341 (p0) cc_final: 0.7921 (p0) REVERT: C 730 GLU cc_start: 0.8000 (tp30) cc_final: 0.7426 (mm-30) REVERT: C 751 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 755 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8180 (tmtt) REVERT: C 771 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7017 (pp20) REVERT: D 247 VAL cc_start: 0.8736 (t) cc_final: 0.8432 (p) REVERT: D 252 LYS cc_start: 0.8215 (tppp) cc_final: 0.7921 (tppp) REVERT: D 254 ILE cc_start: 0.8964 (mm) cc_final: 0.8712 (mt) REVERT: D 301 ASN cc_start: 0.7691 (m110) cc_final: 0.7372 (m110) REVERT: D 328 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8142 (ttm110) REVERT: D 333 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6507 (tm-30) REVERT: D 374 MET cc_start: 0.7996 (tpt) cc_final: 0.7641 (tpp) REVERT: D 415 ASP cc_start: 0.7376 (p0) cc_final: 0.7051 (p0) REVERT: D 423 LEU cc_start: 0.9147 (mt) cc_final: 0.8898 (mt) REVERT: D 426 GLN cc_start: 0.8316 (tp40) cc_final: 0.7892 (tp40) REVERT: D 443 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8346 (mmtp) REVERT: D 444 TYR cc_start: 0.8408 (t80) cc_final: 0.7995 (t80) REVERT: D 448 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7837 (ttmm) REVERT: D 463 GLU cc_start: 0.8116 (tp30) cc_final: 0.7832 (tp30) REVERT: D 489 LYS cc_start: 0.8289 (mppt) cc_final: 0.7929 (mppt) REVERT: D 492 GLU cc_start: 0.7978 (mp0) cc_final: 0.7608 (mp0) REVERT: D 497 ASP cc_start: 0.7752 (t0) cc_final: 0.7519 (t0) REVERT: D 512 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7823 (ttmm) REVERT: D 513 VAL cc_start: 0.8717 (m) cc_final: 0.8415 (p) REVERT: D 517 ASP cc_start: 0.8523 (m-30) cc_final: 0.8314 (m-30) REVERT: D 523 GLU cc_start: 0.7479 (tp30) cc_final: 0.6836 (tp30) REVERT: D 525 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8412 (mmmm) REVERT: D 530 GLU cc_start: 0.7565 (tt0) cc_final: 0.7259 (tt0) REVERT: D 556 TYR cc_start: 0.8059 (p90) cc_final: 0.7788 (p90) REVERT: D 599 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.6967 (mtt-85) REVERT: D 604 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8083 (ttmt) REVERT: D 638 THR cc_start: 0.8621 (t) cc_final: 0.8339 (p) REVERT: D 642 ASN cc_start: 0.8268 (t0) cc_final: 0.7867 (t0) REVERT: D 661 ARG cc_start: 0.6968 (tpt170) cc_final: 0.6645 (tpt170) REVERT: D 690 LEU cc_start: 0.9197 (tp) cc_final: 0.8975 (tt) REVERT: D 694 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8673 (mtmm) REVERT: D 699 LYS cc_start: 0.9204 (tptm) cc_final: 0.8837 (tppp) REVERT: D 717 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7307 (tm-30) REVERT: D 723 GLU cc_start: 0.7684 (mp0) cc_final: 0.7080 (mp0) REVERT: D 751 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7179 (tm-30) REVERT: D 752 LYS cc_start: 0.8784 (tptp) cc_final: 0.8306 (tptp) REVERT: D 755 LYS cc_start: 0.8570 (tttt) cc_final: 0.8296 (tptp) REVERT: D 770 GLU cc_start: 0.7666 (tp30) cc_final: 0.6766 (tp30) REVERT: E 253 GLU cc_start: 0.7576 (pm20) cc_final: 0.7318 (mp0) REVERT: E 297 ARG cc_start: 0.7235 (tpt90) cc_final: 0.6978 (tpt90) REVERT: E 311 ASN cc_start: 0.7580 (m-40) cc_final: 0.7371 (t0) REVERT: E 390 ASN cc_start: 0.7594 (p0) cc_final: 0.7388 (p0) REVERT: E 443 LYS cc_start: 0.8848 (tppt) cc_final: 0.8638 (tppt) REVERT: E 444 TYR cc_start: 0.8402 (t80) cc_final: 0.8011 (t80) REVERT: E 461 CYS cc_start: 0.8139 (m) cc_final: 0.7938 (t) REVERT: E 484 LEU cc_start: 0.8055 (mp) cc_final: 0.7662 (tt) REVERT: E 485 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8166 (mmtt) REVERT: E 488 LEU cc_start: 0.8728 (tt) cc_final: 0.7473 (tt) REVERT: E 490 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7636 (t0) REVERT: E 492 GLU cc_start: 0.7701 (mp0) cc_final: 0.7107 (mp0) REVERT: E 507 PHE cc_start: 0.5799 (p90) cc_final: 0.5564 (p90) REVERT: E 512 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7917 (ttpt) REVERT: E 530 GLU cc_start: 0.7548 (tt0) cc_final: 0.6939 (tt0) REVERT: E 556 TYR cc_start: 0.8272 (p90) cc_final: 0.7880 (p90) REVERT: E 619 ASP cc_start: 0.7785 (m-30) cc_final: 0.7279 (m-30) REVERT: E 642 ASN cc_start: 0.8337 (t0) cc_final: 0.8055 (t0) REVERT: E 661 ARG cc_start: 0.7059 (tpt90) cc_final: 0.6593 (tpt170) REVERT: E 663 ASP cc_start: 0.8430 (p0) cc_final: 0.8104 (p0) REVERT: E 664 GLU cc_start: 0.7887 (tt0) cc_final: 0.7460 (tt0) REVERT: E 691 GLU cc_start: 0.8225 (tp30) cc_final: 0.8011 (tp30) REVERT: E 695 LYS cc_start: 0.8514 (tmtt) cc_final: 0.8314 (tptm) REVERT: E 696 CYS cc_start: 0.8040 (t) cc_final: 0.7800 (t) REVERT: E 715 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7669 (ttp80) REVERT: E 723 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7628 (mm-30) REVERT: E 745 VAL cc_start: 0.8392 (t) cc_final: 0.7856 (m) REVERT: E 752 LYS cc_start: 0.8866 (tmtt) cc_final: 0.8534 (ttmm) REVERT: E 755 LYS cc_start: 0.8731 (tttm) cc_final: 0.8504 (tttm) REVERT: F 292 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8330 (mttp) REVERT: F 308 LEU cc_start: 0.8436 (mp) cc_final: 0.8141 (mp) REVERT: F 393 ASN cc_start: 0.8432 (m-40) cc_final: 0.8189 (m-40) REVERT: F 406 ASP cc_start: 0.6862 (t0) cc_final: 0.6350 (t0) REVERT: F 463 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7812 (mm-30) REVERT: F 485 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7736 (mmtt) REVERT: F 490 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7477 (t0) REVERT: F 513 VAL cc_start: 0.8606 (m) cc_final: 0.8360 (p) REVERT: F 536 LEU cc_start: 0.8697 (mm) cc_final: 0.8412 (tp) REVERT: F 540 GLU cc_start: 0.7282 (pp20) cc_final: 0.6963 (pp20) REVERT: F 556 TYR cc_start: 0.8247 (p90) cc_final: 0.7947 (p90) REVERT: F 572 THR cc_start: 0.8424 (m) cc_final: 0.8115 (p) REVERT: F 573 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6829 (tm-30) REVERT: F 585 GLU cc_start: 0.6869 (pt0) cc_final: 0.6644 (pp20) REVERT: F 621 LEU cc_start: 0.7934 (mt) cc_final: 0.7372 (mp) REVERT: F 642 ASN cc_start: 0.8287 (t0) cc_final: 0.7967 (t0) REVERT: F 659 THR cc_start: 0.8574 (t) cc_final: 0.8247 (m) REVERT: F 661 ARG cc_start: 0.7267 (tpt170) cc_final: 0.6036 (tpt170) REVERT: F 663 ASP cc_start: 0.8177 (p0) cc_final: 0.7506 (p0) REVERT: F 676 ASP cc_start: 0.7595 (p0) cc_final: 0.7301 (p0) REVERT: F 687 ASN cc_start: 0.8736 (t0) cc_final: 0.8497 (t0) REVERT: F 691 GLU cc_start: 0.8126 (tp30) cc_final: 0.7864 (tp30) REVERT: F 699 LYS cc_start: 0.9224 (tppp) cc_final: 0.9022 (tptp) REVERT: F 728 CYS cc_start: 0.7731 (m) cc_final: 0.7440 (m) REVERT: F 751 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7210 (tp30) REVERT: F 752 LYS cc_start: 0.8661 (tptp) cc_final: 0.8419 (tptp) outliers start: 46 outliers final: 22 residues processed: 1012 average time/residue: 0.4970 time to fit residues: 732.8037 Evaluate side-chains 949 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 921 time to evaluate : 2.733 ------------------------------------------------------------------------------- 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 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 331 PHE Chi-restraints excluded: chain F residue 453 VAL 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 163 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 200 optimal weight: 0.0870 chunk 81 optimal weight: 20.0000 chunk 294 optimal weight: 6.9990 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 292 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 687 ASN ** F 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25782 Z= 0.220 Angle : 0.688 12.300 34986 Z= 0.343 Chirality : 0.045 0.223 4020 Planarity : 0.006 0.076 4488 Dihedral : 12.946 157.295 3816 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.78 % Allowed : 16.70 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3240 helix: 0.86 (0.13), residues: 1554 sheet: 0.24 (0.30), residues: 354 loop : -0.48 (0.19), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 515 HIS 0.027 0.002 HIS B 285 PHE 0.035 0.002 PHE B 507 TYR 0.029 0.002 TYR B 556 ARG 0.011 0.001 ARG F 775 *********************** 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 fitting. rotamer outliers: 75 poor density : 953 time to evaluate : 2.842 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 333 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 335 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7679 (mtp-110) REVERT: A 429 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7565 (mmm-85) REVERT: A 438 ASP cc_start: 0.7670 (p0) cc_final: 0.7446 (p0) REVERT: A 443 LYS cc_start: 0.8788 (mmpt) cc_final: 0.8225 (mmmm) REVERT: A 444 TYR cc_start: 0.8276 (t80) cc_final: 0.7639 (t80) REVERT: A 448 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7715 (mtmm) REVERT: A 492 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 512 LYS cc_start: 0.8473 (tttp) cc_final: 0.8095 (tttm) REVERT: A 514 TYR cc_start: 0.8357 (m-10) cc_final: 0.8102 (m-10) REVERT: A 523 GLU cc_start: 0.7394 (tp30) cc_final: 0.6928 (tp30) REVERT: A 530 GLU cc_start: 0.7591 (tt0) cc_final: 0.7343 (tt0) REVERT: A 540 GLU cc_start: 0.7326 (pp20) cc_final: 0.6985 (pp20) REVERT: A 548 SER cc_start: 0.8738 (m) cc_final: 0.8224 (p) REVERT: A 556 TYR cc_start: 0.8088 (p90) cc_final: 0.7797 (p90) REVERT: A 572 THR cc_start: 0.8410 (m) cc_final: 0.8006 (p) REVERT: A 586 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8717 (tp) REVERT: A 595 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 663 ASP cc_start: 0.7623 (p0) cc_final: 0.7097 (p0) REVERT: A 695 LYS cc_start: 0.8614 (tmtt) cc_final: 0.8311 (tptp) REVERT: A 698 LYS cc_start: 0.8862 (ptmm) cc_final: 0.8432 (ptpp) REVERT: A 717 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 730 GLU cc_start: 0.8054 (tp30) cc_final: 0.7116 (mm-30) REVERT: A 751 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6947 (tm-30) REVERT: A 752 LYS cc_start: 0.8782 (tttm) cc_final: 0.8402 (ttmm) REVERT: A 755 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8328 (ttmt) REVERT: A 770 GLU cc_start: 0.7308 (mp0) cc_final: 0.7081 (mp0) REVERT: B 311 ASN cc_start: 0.7573 (t0) cc_final: 0.7351 (t0) REVERT: B 328 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7827 (ttm110) REVERT: B 333 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6882 (tm-30) REVERT: B 391 ARG cc_start: 0.7955 (ptt-90) cc_final: 0.7220 (ptt-90) REVERT: B 421 ASP cc_start: 0.8222 (t0) cc_final: 0.7927 (t0) REVERT: B 430 MET cc_start: 0.7441 (ptt) cc_final: 0.7231 (ptt) REVERT: B 434 ARG cc_start: 0.7694 (mmm-85) cc_final: 0.7456 (mmm-85) REVERT: B 463 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7740 (mm-30) REVERT: B 486 VAL cc_start: 0.8977 (p) cc_final: 0.8776 (m) REVERT: B 490 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7451 (t0) REVERT: B 493 SER cc_start: 0.8713 (t) cc_final: 0.8475 (p) REVERT: B 497 ASP cc_start: 0.7357 (t0) cc_final: 0.6869 (t0) REVERT: B 525 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8162 (mmtp) REVERT: B 534 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8630 (tp) REVERT: B 540 GLU cc_start: 0.7485 (pp20) cc_final: 0.7248 (pp20) REVERT: B 548 SER cc_start: 0.8728 (t) cc_final: 0.8410 (p) REVERT: B 585 GLU cc_start: 0.7458 (pt0) cc_final: 0.7127 (pp20) REVERT: B 587 PHE cc_start: 0.7420 (t80) cc_final: 0.7170 (t80) REVERT: B 600 GLU cc_start: 0.7538 (pp20) cc_final: 0.7192 (pp20) REVERT: B 617 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7510 (mp0) REVERT: B 638 THR cc_start: 0.8462 (t) cc_final: 0.8129 (p) REVERT: B 642 ASN cc_start: 0.8273 (t0) cc_final: 0.7979 (t0) REVERT: B 643 GLU cc_start: 0.7906 (tp30) cc_final: 0.7612 (tp30) REVERT: B 661 ARG cc_start: 0.6776 (tpt170) cc_final: 0.6500 (tpm170) REVERT: B 677 ARG cc_start: 0.7399 (mmt-90) cc_final: 0.6965 (mmt-90) REVERT: B 689 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8593 (mtm-85) REVERT: B 694 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8463 (mtpt) REVERT: B 695 LYS cc_start: 0.8447 (tmtt) cc_final: 0.8208 (tptm) REVERT: B 696 CYS cc_start: 0.7938 (t) cc_final: 0.7698 (t) REVERT: B 723 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7202 (mt-10) REVERT: B 751 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7350 (tp30) REVERT: B 752 LYS cc_start: 0.8707 (tttm) cc_final: 0.8499 (ttmm) REVERT: B 765 MET cc_start: 0.7794 (mtp) cc_final: 0.7534 (mtp) REVERT: C 252 LYS cc_start: 0.8348 (mttm) cc_final: 0.8145 (mttm) REVERT: C 255 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7349 (tm-30) REVERT: C 262 GLU cc_start: 0.7923 (tp30) cc_final: 0.7695 (tm-30) REVERT: C 267 GLN cc_start: 0.8597 (pt0) cc_final: 0.8342 (pt0) REVERT: C 324 GLU cc_start: 0.7621 (mp0) cc_final: 0.6790 (mp0) REVERT: C 333 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6939 (tm-30) REVERT: C 382 LYS cc_start: 0.7098 (mtmt) cc_final: 0.6849 (mtmm) REVERT: C 393 ASN cc_start: 0.8408 (m-40) cc_final: 0.8122 (m-40) REVERT: C 421 ASP cc_start: 0.8036 (t0) cc_final: 0.7618 (t0) REVERT: C 426 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8042 (mm-40) REVERT: C 443 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8429 (mmtp) REVERT: C 463 GLU cc_start: 0.8044 (tp30) cc_final: 0.7755 (tp30) REVERT: C 484 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8184 (mm) REVERT: C 488 LEU cc_start: 0.7803 (tp) cc_final: 0.7399 (tt) REVERT: C 490 ASP cc_start: 0.7981 (t0) cc_final: 0.7357 (t0) REVERT: C 492 GLU cc_start: 0.7827 (mp0) cc_final: 0.7532 (mp0) REVERT: C 493 SER cc_start: 0.8774 (t) cc_final: 0.8338 (p) REVERT: C 512 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7939 (mmmt) REVERT: C 522 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 582 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8277 (mmmm) REVERT: C 595 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7756 (mt-10) REVERT: C 599 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7698 (mtt-85) REVERT: C 600 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: C 661 ARG cc_start: 0.7018 (tpt170) cc_final: 0.6372 (tpt170) REVERT: C 671 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7834 (ttm-80) REVERT: C 697 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8782 (t) REVERT: C 715 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7687 (ttp80) REVERT: C 730 GLU cc_start: 0.7979 (tp30) cc_final: 0.7446 (mm-30) REVERT: C 751 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7179 (tm-30) REVERT: C 755 LYS cc_start: 0.8572 (tmtt) cc_final: 0.8326 (tmtt) REVERT: D 252 LYS cc_start: 0.8165 (tppp) cc_final: 0.7880 (tppp) REVERT: D 301 ASN cc_start: 0.7739 (m110) cc_final: 0.7373 (m110) REVERT: D 328 ARG cc_start: 0.8384 (ttm110) cc_final: 0.8058 (ttm110) REVERT: D 333 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6588 (tm-30) REVERT: D 374 MET cc_start: 0.7975 (tpt) cc_final: 0.7600 (tpp) REVERT: D 415 ASP cc_start: 0.7325 (p0) cc_final: 0.7031 (p0) REVERT: D 426 GLN cc_start: 0.8332 (tp40) cc_final: 0.7894 (tp40) REVERT: D 443 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8264 (mmtp) REVERT: D 444 TYR cc_start: 0.8325 (t80) cc_final: 0.8118 (t80) REVERT: D 448 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7811 (ttmm) REVERT: D 463 GLU cc_start: 0.8169 (tp30) cc_final: 0.7730 (mm-30) REVERT: D 512 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7853 (ttmm) REVERT: D 523 GLU cc_start: 0.7479 (tp30) cc_final: 0.6808 (tp30) REVERT: D 556 TYR cc_start: 0.7929 (p90) cc_final: 0.7690 (p90) REVERT: D 595 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7429 (tm-30) REVERT: D 600 GLU cc_start: 0.7411 (pp20) cc_final: 0.6984 (pp20) REVERT: D 604 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8185 (ttmt) REVERT: D 638 THR cc_start: 0.8637 (t) cc_final: 0.8310 (p) REVERT: D 642 ASN cc_start: 0.8255 (t0) cc_final: 0.7832 (t0) REVERT: D 687 ASN cc_start: 0.8553 (t0) cc_final: 0.8350 (t0) REVERT: D 699 LYS cc_start: 0.9177 (tptm) cc_final: 0.8788 (tppp) REVERT: D 717 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7359 (tm-30) REVERT: D 730 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7585 (mm-30) REVERT: D 751 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7107 (tm-30) REVERT: D 755 LYS cc_start: 0.8537 (tttt) cc_final: 0.8238 (tptp) REVERT: D 768 TYR cc_start: 0.5939 (m-10) cc_final: 0.5477 (m-10) REVERT: D 771 GLU cc_start: 0.7776 (pp20) cc_final: 0.7409 (pp20) REVERT: E 292 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8248 (mtmm) REVERT: E 297 ARG cc_start: 0.7311 (tpt90) cc_final: 0.7007 (tpt90) REVERT: E 390 ASN cc_start: 0.7588 (p0) cc_final: 0.7327 (p0) REVERT: E 443 LYS cc_start: 0.8807 (tppt) cc_final: 0.8327 (tppt) REVERT: E 444 TYR cc_start: 0.8365 (t80) cc_final: 0.8043 (t80) REVERT: E 484 LEU cc_start: 0.8023 (mp) cc_final: 0.7799 (tp) REVERT: E 490 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7826 (t0) REVERT: E 512 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7787 (ttpt) REVERT: E 530 GLU cc_start: 0.7339 (tt0) cc_final: 0.7029 (tt0) REVERT: E 556 TYR cc_start: 0.8265 (p90) cc_final: 0.7918 (p90) REVERT: E 604 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8460 (ttmt) REVERT: E 619 ASP cc_start: 0.7804 (m-30) cc_final: 0.7090 (m-30) REVERT: E 642 ASN cc_start: 0.8335 (t0) cc_final: 0.8021 (t0) REVERT: E 661 ARG cc_start: 0.6821 (tpt90) cc_final: 0.6148 (tpt170) REVERT: E 663 ASP cc_start: 0.8379 (p0) cc_final: 0.7845 (p0) REVERT: E 664 GLU cc_start: 0.7878 (tt0) cc_final: 0.7401 (tt0) REVERT: E 691 GLU cc_start: 0.8139 (tp30) cc_final: 0.7928 (tp30) REVERT: E 704 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7331 (tm-30) REVERT: E 715 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7677 (ttp80) REVERT: E 723 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7494 (mm-30) REVERT: E 745 VAL cc_start: 0.8396 (t) cc_final: 0.7947 (m) REVERT: E 752 LYS cc_start: 0.8862 (tmtt) cc_final: 0.8420 (tmtt) REVERT: E 755 LYS cc_start: 0.8715 (tttm) cc_final: 0.8496 (tttm) REVERT: E 771 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7227 (pp20) REVERT: F 253 GLU cc_start: 0.7643 (pm20) cc_final: 0.7406 (pm20) REVERT: F 311 ASN cc_start: 0.7687 (t0) cc_final: 0.7353 (t0) REVERT: F 393 ASN cc_start: 0.8524 (m-40) cc_final: 0.8281 (m-40) REVERT: F 444 TYR cc_start: 0.8615 (t80) cc_final: 0.7999 (t80) REVERT: F 468 THR cc_start: 0.8432 (m) cc_final: 0.7932 (p) REVERT: F 485 LYS cc_start: 0.8313 (mmtt) cc_final: 0.7764 (mmtt) REVERT: F 490 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7423 (t0) REVERT: F 513 VAL cc_start: 0.8648 (m) cc_final: 0.8428 (p) REVERT: F 536 LEU cc_start: 0.8709 (mm) cc_final: 0.8414 (tp) REVERT: F 540 GLU cc_start: 0.7273 (pp20) cc_final: 0.6955 (pp20) REVERT: F 572 THR cc_start: 0.8479 (m) cc_final: 0.7863 (p) REVERT: F 604 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8576 (ttmm) REVERT: F 642 ASN cc_start: 0.8296 (t0) cc_final: 0.7956 (t0) REVERT: F 661 ARG cc_start: 0.7162 (tpt170) cc_final: 0.5915 (tpt170) REVERT: F 663 ASP cc_start: 0.8153 (p0) cc_final: 0.7405 (p0) REVERT: F 687 ASN cc_start: 0.8727 (t0) cc_final: 0.8489 (t0) REVERT: F 723 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7236 (mt-10) REVERT: F 729 GLN cc_start: 0.8387 (mt0) cc_final: 0.8017 (mt0) REVERT: F 751 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7030 (tm-30) REVERT: F 752 LYS cc_start: 0.8646 (tptp) cc_final: 0.8258 (tptp) outliers start: 75 outliers final: 43 residues processed: 973 average time/residue: 0.4680 time to fit residues: 654.6959 Evaluate side-chains 963 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 909 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 484 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 551 LYS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 659 THR 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 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 534 LEU Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 694 LYS Chi-restraints excluded: chain B residue 774 LEU 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 D residue 762 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 314 SER 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 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 291 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 154 optimal weight: 0.0050 chunk 280 optimal weight: 0.0980 chunk 84 optimal weight: 0.0010 overall best weight: 0.6202 ------------------------------------------------------------------------------- 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 687 ASN ** C 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS F 393 ASN F 426 GLN ** F 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25782 Z= 0.203 Angle : 0.661 10.574 34986 Z= 0.328 Chirality : 0.044 0.204 4020 Planarity : 0.005 0.077 4488 Dihedral : 12.557 159.484 3816 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.59 % Allowed : 18.74 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3240 helix: 1.02 (0.13), residues: 1554 sheet: 0.39 (0.30), residues: 348 loop : -0.35 (0.19), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 515 HIS 0.010 0.001 HIS B 285 PHE 0.035 0.002 PHE D 587 TYR 0.033 0.002 TYR C 444 ARG 0.009 0.001 ARG F 775 *********************** 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 1008 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 911 time to evaluate : 3.024 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: 0.7870 (tp30) cc_final: 0.7408 (tm-30) REVERT: A 333 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6894 (tm-30) REVERT: A 335 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7670 (mtp-110) REVERT: A 429 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7568 (mmm-85) REVERT: A 443 LYS cc_start: 0.8733 (mmpt) cc_final: 0.8417 (tppt) REVERT: A 463 GLU cc_start: 0.7967 (tp30) cc_final: 0.7478 (tp30) REVERT: A 485 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7854 (mmtt) REVERT: A 488 LEU cc_start: 0.8085 (tp) cc_final: 0.7768 (tt) REVERT: A 492 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: A 512 LYS cc_start: 0.8469 (tttp) cc_final: 0.8111 (tttm) REVERT: A 514 TYR cc_start: 0.8357 (m-10) cc_final: 0.7948 (m-10) REVERT: A 523 GLU cc_start: 0.7432 (tp30) cc_final: 0.6946 (tp30) REVERT: A 525 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8427 (ttmt) REVERT: A 530 GLU cc_start: 0.7522 (tt0) cc_final: 0.7115 (tt0) REVERT: A 540 GLU cc_start: 0.7322 (pp20) cc_final: 0.7011 (pp20) REVERT: A 548 SER cc_start: 0.8710 (m) cc_final: 0.8228 (p) REVERT: A 556 TYR cc_start: 0.8051 (p90) cc_final: 0.7743 (p90) REVERT: A 572 THR cc_start: 0.8359 (m) cc_final: 0.7994 (p) REVERT: A 586 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8618 (tp) REVERT: A 595 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7916 (mt-10) REVERT: A 661 ARG cc_start: 0.7463 (mmm160) cc_final: 0.7121 (mmm160) REVERT: A 663 ASP cc_start: 0.7574 (p0) cc_final: 0.6936 (p0) REVERT: A 665 ILE cc_start: 0.8646 (mm) cc_final: 0.8436 (tt) REVERT: A 695 LYS cc_start: 0.8603 (tmtt) cc_final: 0.8347 (tptp) REVERT: A 698 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8477 (ptpp) REVERT: A 717 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 737 MET cc_start: 0.6360 (ttm) cc_final: 0.5909 (ttm) REVERT: A 751 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6941 (tm-30) REVERT: A 752 LYS cc_start: 0.8797 (tttm) cc_final: 0.8416 (ttmm) REVERT: A 755 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8306 (ttmt) REVERT: B 301 ASN cc_start: 0.8188 (t0) cc_final: 0.7896 (t0) REVERT: B 311 ASN cc_start: 0.7606 (t0) cc_final: 0.7393 (t0) REVERT: B 328 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7818 (ttm110) REVERT: B 333 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6922 (tm-30) REVERT: B 391 ARG cc_start: 0.7953 (ptt-90) cc_final: 0.7338 (ptt-90) REVERT: B 421 ASP cc_start: 0.8245 (t0) cc_final: 0.7876 (t0) REVERT: B 448 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7857 (mtpt) REVERT: B 463 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 468 THR cc_start: 0.8549 (m) cc_final: 0.8010 (p) REVERT: B 486 VAL cc_start: 0.9030 (p) cc_final: 0.8810 (m) REVERT: B 490 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7490 (t0) REVERT: B 492 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 493 SER cc_start: 0.8770 (t) cc_final: 0.8459 (p) REVERT: B 497 ASP cc_start: 0.7453 (t0) cc_final: 0.7083 (t70) REVERT: B 525 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8169 (mmtp) REVERT: B 530 GLU cc_start: 0.7747 (tt0) cc_final: 0.6980 (tt0) REVERT: B 534 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8680 (tp) REVERT: B 540 GLU cc_start: 0.7462 (pp20) cc_final: 0.7187 (pp20) REVERT: B 548 SER cc_start: 0.8723 (t) cc_final: 0.8401 (p) REVERT: B 582 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8175 (mtmm) REVERT: B 585 GLU cc_start: 0.7459 (pt0) cc_final: 0.7108 (pp20) REVERT: B 587 PHE cc_start: 0.7431 (t80) cc_final: 0.7181 (t80) REVERT: B 600 GLU cc_start: 0.7539 (pp20) cc_final: 0.7157 (pp20) REVERT: B 617 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7443 (mm-30) REVERT: B 638 THR cc_start: 0.8453 (t) cc_final: 0.8138 (p) REVERT: B 642 ASN cc_start: 0.8284 (t0) cc_final: 0.7960 (t0) REVERT: B 643 GLU cc_start: 0.7925 (tp30) cc_final: 0.7588 (tp30) REVERT: B 678 HIS cc_start: 0.7754 (m170) cc_final: 0.7463 (m170) REVERT: B 694 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8442 (mtpt) REVERT: B 723 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 751 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7356 (tp30) REVERT: B 752 LYS cc_start: 0.8692 (tttm) cc_final: 0.8490 (ttmm) REVERT: C 255 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7302 (tm-30) REVERT: C 324 GLU cc_start: 0.7511 (mp0) cc_final: 0.6669 (mp0) REVERT: C 333 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6943 (tp30) REVERT: C 382 LYS cc_start: 0.7211 (mtmt) cc_final: 0.6920 (mtmm) REVERT: C 393 ASN cc_start: 0.8422 (m-40) cc_final: 0.8162 (m-40) REVERT: C 406 ASP cc_start: 0.6777 (t0) cc_final: 0.6512 (m-30) REVERT: C 421 ASP cc_start: 0.8093 (t0) cc_final: 0.7758 (t0) REVERT: C 426 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8018 (mm-40) REVERT: C 443 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8411 (mmtp) REVERT: C 463 GLU cc_start: 0.8045 (tp30) cc_final: 0.7725 (tp30) REVERT: C 484 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8149 (mm) REVERT: C 488 LEU cc_start: 0.7852 (tp) cc_final: 0.7261 (tt) REVERT: C 490 ASP cc_start: 0.7985 (t0) cc_final: 0.7363 (t0) REVERT: C 492 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: C 493 SER cc_start: 0.8752 (t) cc_final: 0.8430 (p) REVERT: C 512 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7910 (mmmt) REVERT: C 522 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 582 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8321 (mmmm) REVERT: C 595 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7758 (mt-10) REVERT: C 599 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7700 (mtt-85) REVERT: C 661 ARG cc_start: 0.7084 (tpt170) cc_final: 0.6656 (tpt170) REVERT: C 715 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7593 (ttp80) REVERT: C 730 GLU cc_start: 0.7958 (tp30) cc_final: 0.7685 (mm-30) REVERT: C 737 MET cc_start: 0.6484 (mtt) cc_final: 0.6246 (mtt) REVERT: C 751 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7168 (tm-30) REVERT: C 755 LYS cc_start: 0.8545 (tmtt) cc_final: 0.8294 (tmtt) REVERT: C 771 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7044 (pp20) REVERT: D 252 LYS cc_start: 0.8125 (tppp) cc_final: 0.7775 (tppp) REVERT: D 301 ASN cc_start: 0.7759 (m110) cc_final: 0.7376 (m110) REVERT: D 328 ARG cc_start: 0.8368 (ttm110) cc_final: 0.8027 (ttm110) REVERT: D 333 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6592 (tm-30) REVERT: D 374 MET cc_start: 0.7957 (tpt) cc_final: 0.7551 (tpp) REVERT: D 406 ASP cc_start: 0.6902 (t0) cc_final: 0.6680 (t0) REVERT: D 415 ASP cc_start: 0.7302 (p0) cc_final: 0.7070 (p0) REVERT: D 423 LEU cc_start: 0.9046 (mt) cc_final: 0.8845 (mt) REVERT: D 425 LYS cc_start: 0.8722 (mttm) cc_final: 0.8439 (ttmm) REVERT: D 426 GLN cc_start: 0.8356 (tp40) cc_final: 0.7958 (tp40) REVERT: D 434 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7357 (mtt90) REVERT: D 443 LYS cc_start: 0.8577 (mmtp) cc_final: 0.8231 (mmtp) REVERT: D 444 TYR cc_start: 0.8341 (t80) cc_final: 0.8044 (t80) REVERT: D 448 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7812 (ttmm) REVERT: D 463 GLU cc_start: 0.8137 (tp30) cc_final: 0.7859 (tp30) REVERT: D 488 LEU cc_start: 0.8118 (tp) cc_final: 0.7782 (tt) REVERT: D 492 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: D 522 GLU cc_start: 0.7721 (tp30) cc_final: 0.7492 (mm-30) REVERT: D 523 GLU cc_start: 0.7487 (tp30) cc_final: 0.6807 (tp30) REVERT: D 525 LYS cc_start: 0.8302 (mmmm) cc_final: 0.8080 (tppp) REVERT: D 527 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8190 (mtpp) REVERT: D 556 TYR cc_start: 0.7862 (p90) cc_final: 0.7655 (p90) REVERT: D 585 GLU cc_start: 0.7267 (pt0) cc_final: 0.7001 (pp20) REVERT: D 595 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7229 (tm-30) REVERT: D 600 GLU cc_start: 0.7413 (pp20) cc_final: 0.6981 (pp20) REVERT: D 604 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8298 (ttmt) REVERT: D 638 THR cc_start: 0.8652 (t) cc_final: 0.8329 (p) REVERT: D 642 ASN cc_start: 0.8267 (t0) cc_final: 0.7852 (t0) REVERT: D 661 ARG cc_start: 0.7158 (tpt170) cc_final: 0.6797 (tpt170) REVERT: D 691 GLU cc_start: 0.8131 (tp30) cc_final: 0.7319 (tp30) REVERT: D 699 LYS cc_start: 0.9144 (tptm) cc_final: 0.8769 (tppp) REVERT: D 751 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7235 (tp30) REVERT: D 755 LYS cc_start: 0.8576 (tttt) cc_final: 0.8271 (tptp) REVERT: D 768 TYR cc_start: 0.5956 (m-10) cc_final: 0.5590 (m-10) REVERT: D 770 GLU cc_start: 0.7945 (tp30) cc_final: 0.7739 (mm-30) REVERT: D 771 GLU cc_start: 0.7776 (pp20) cc_final: 0.7541 (pp20) REVERT: E 292 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8253 (mttp) REVERT: E 297 ARG cc_start: 0.7263 (tpt90) cc_final: 0.7006 (tpt90) REVERT: E 374 MET cc_start: 0.7949 (tpp) cc_final: 0.7539 (tpt) REVERT: E 382 LYS cc_start: 0.7107 (mtpt) cc_final: 0.6705 (mtpt) REVERT: E 443 LYS cc_start: 0.8823 (tppt) cc_final: 0.8389 (tppt) REVERT: E 444 TYR cc_start: 0.8222 (t80) cc_final: 0.8010 (t80) REVERT: E 484 LEU cc_start: 0.8094 (mp) cc_final: 0.7820 (tt) REVERT: E 488 LEU cc_start: 0.8862 (tt) cc_final: 0.8399 (tp) REVERT: E 490 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7640 (t0) REVERT: E 492 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: E 512 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7681 (ttpt) REVERT: E 515 TRP cc_start: 0.8924 (m100) cc_final: 0.8394 (m100) REVERT: E 556 TYR cc_start: 0.8164 (p90) cc_final: 0.7806 (p90) REVERT: E 563 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8389 (ptmt) REVERT: E 585 GLU cc_start: 0.6855 (pt0) cc_final: 0.6518 (pp20) REVERT: E 617 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7525 (mm-30) REVERT: E 619 ASP cc_start: 0.7835 (m-30) cc_final: 0.7573 (m-30) REVERT: E 642 ASN cc_start: 0.8327 (t0) cc_final: 0.8060 (t0) REVERT: E 660 ASN cc_start: 0.8542 (p0) cc_final: 0.7547 (p0) REVERT: E 661 ARG cc_start: 0.6662 (tpt90) cc_final: 0.6022 (tpt170) REVERT: E 663 ASP cc_start: 0.8295 (p0) cc_final: 0.7908 (p0) REVERT: E 715 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7713 (ttp80) REVERT: E 745 VAL cc_start: 0.8424 (t) cc_final: 0.7993 (m) REVERT: E 751 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7317 (tp30) REVERT: E 752 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8474 (tmtt) REVERT: E 771 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7395 (pp20) REVERT: F 285 HIS cc_start: 0.6798 (m-70) cc_final: 0.6551 (m-70) REVERT: F 311 ASN cc_start: 0.7645 (t0) cc_final: 0.7313 (t0) REVERT: F 331 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7636 (t80) REVERT: F 391 ARG cc_start: 0.7686 (mtm180) cc_final: 0.7419 (mtm-85) REVERT: F 393 ASN cc_start: 0.8490 (m110) cc_final: 0.8255 (m110) REVERT: F 444 TYR cc_start: 0.8586 (t80) cc_final: 0.7961 (t80) REVERT: F 468 THR cc_start: 0.8422 (m) cc_final: 0.7948 (p) REVERT: F 485 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7850 (mmtt) REVERT: F 488 LEU cc_start: 0.7755 (tp) cc_final: 0.7441 (tt) REVERT: F 490 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7481 (t0) REVERT: F 536 LEU cc_start: 0.8754 (mm) cc_final: 0.8436 (tp) REVERT: F 540 GLU cc_start: 0.7301 (pp20) cc_final: 0.6975 (pp20) REVERT: F 572 THR cc_start: 0.8515 (m) cc_final: 0.8129 (p) REVERT: F 642 ASN cc_start: 0.8213 (t0) cc_final: 0.7887 (t0) REVERT: F 661 ARG cc_start: 0.7154 (tpt170) cc_final: 0.5809 (tpt90) REVERT: F 663 ASP cc_start: 0.8189 (p0) cc_final: 0.7587 (p0) REVERT: F 687 ASN cc_start: 0.8715 (t0) cc_final: 0.8456 (t0) REVERT: F 697 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8957 (t) REVERT: F 723 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7156 (mt-10) REVERT: F 729 GLN cc_start: 0.8341 (mt0) cc_final: 0.8019 (mt0) REVERT: F 746 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7037 (mp0) REVERT: F 751 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7009 (tm-30) REVERT: F 752 LYS cc_start: 0.8689 (tptp) cc_final: 0.8264 (tptp) outliers start: 97 outliers final: 45 residues processed: 944 average time/residue: 0.4634 time to fit residues: 623.4905 Evaluate side-chains 928 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 867 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 282 ILE 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 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 492 GLU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 694 LYS Chi-restraints excluded: chain B residue 774 LEU 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 666 ASP Chi-restraints excluded: chain C residue 774 LEU 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 513 VAL Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 490 ASP Chi-restraints excluded: chain E residue 492 GLU 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 331 PHE Chi-restraints excluded: chain F residue 390 ASN 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 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 774 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 281 optimal weight: 0.0170 chunk 79 optimal weight: 4.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: