Starting phenix.real_space_refine on Fri Jan 24 14:53:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6l_42995/01_2025/8v6l_42995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6l_42995/01_2025/8v6l_42995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v6l_42995/01_2025/8v6l_42995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6l_42995/01_2025/8v6l_42995.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6l_42995/01_2025/8v6l_42995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6l_42995/01_2025/8v6l_42995.cif" } resolution = 3.68 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= 0.030 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 20 5.49 5 S 136 5.16 5 Na 3 4.78 5 C 14724 2.51 5 N 3552 2.21 5 O 3952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 22387 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "B" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "C" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "D" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "A" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 283 Unusual residues: {' NA': 2, 'I8E': 1, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 334 Unusual residues: {' NA': 1, 'I8E': 1, 'POV': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 281 Unusual residues: {'I8E': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'I8E': 1, 'POV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.42, per 1000 atoms: 0.60 Number of scatterers: 22387 At special positions: 0 Unit cell: (136.95, 136.95, 124.5, 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 136 16.00 P 20 15.00 Na 3 11.00 O 3952 8.00 N 3552 7.00 C 14724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.47 Conformation dependent library (CDL) restraints added in 2.8 seconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 8 sheets defined 64.1% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.510A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 147 Processing helix chain 'A' and resid 152 through 163 removed outlier: 4.516A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.886A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.610A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.570A pdb=" N THR A 336 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.568A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 437 through 458 Processing helix chain 'A' and resid 480 through 508 removed outlier: 3.755A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 543 removed outlier: 3.962A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 562 removed outlier: 4.058A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.658A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 Processing helix chain 'A' and resid 574 through 584 removed outlier: 3.949A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 609 removed outlier: 4.340A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.767A pdb=" N ASP A 615 " --> pdb=" O CYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 651 through 666 Processing helix chain 'A' and resid 669 through 687 removed outlier: 3.805A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 4.182A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.545A pdb=" N TRP A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 131 through 147 Processing helix chain 'B' and resid 152 through 163 removed outlier: 4.516A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.889A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.623A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.577A pdb=" N THR B 336 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.572A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 437 through 458 Processing helix chain 'B' and resid 480 through 508 removed outlier: 3.759A pdb=" N LEU B 485 " --> pdb=" O TRP B 481 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 519 through 543 removed outlier: 3.956A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 562 removed outlier: 4.075A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.675A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 573 Processing helix chain 'B' and resid 574 through 586 removed outlier: 4.104A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 609 removed outlier: 4.344A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.775A pdb=" N ASP B 615 " --> pdb=" O CYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 651 through 666 Processing helix chain 'B' and resid 669 through 687 removed outlier: 3.872A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 4.193A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'B' and resid 738 through 750 removed outlier: 3.521A pdb=" N TRP B 742 " --> pdb=" O LYS B 738 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 131 through 147 Processing helix chain 'C' and resid 152 through 163 removed outlier: 4.519A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.887A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.613A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.575A pdb=" N THR C 336 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.566A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 437 through 458 Processing helix chain 'C' and resid 480 through 508 removed outlier: 3.763A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 519 through 543 removed outlier: 3.968A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 562 removed outlier: 4.072A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 removed outlier: 3.667A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 573 Processing helix chain 'C' and resid 574 through 584 removed outlier: 4.022A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 609 removed outlier: 4.345A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 removed outlier: 3.770A pdb=" N ASP C 615 " --> pdb=" O CYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 651 through 666 Processing helix chain 'C' and resid 669 through 687 removed outlier: 3.831A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 4.184A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'C' and resid 738 through 750 removed outlier: 3.544A pdb=" N TRP C 742 " --> pdb=" O LYS C 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 131 through 147 Processing helix chain 'D' and resid 152 through 162 removed outlier: 4.511A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.892A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.614A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.579A pdb=" N THR D 336 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.569A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 437 through 458 Processing helix chain 'D' and resid 480 through 508 removed outlier: 3.766A pdb=" N LEU D 485 " --> pdb=" O TRP D 481 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 519 through 543 removed outlier: 3.969A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 562 removed outlier: 4.076A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.670A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 573 Processing helix chain 'D' and resid 574 through 584 removed outlier: 4.021A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 609 removed outlier: 4.341A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 removed outlier: 3.788A pdb=" N ASP D 615 " --> pdb=" O CYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 651 through 666 Processing helix chain 'D' and resid 669 through 687 removed outlier: 3.827A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 4.184A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 Processing helix chain 'D' and resid 738 through 750 removed outlier: 3.529A pdb=" N TRP D 742 " --> pdb=" O LYS D 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.722A pdb=" N TYR A 390 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AA4, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.723A pdb=" N TYR B 390 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 385 through 386 Processing sheet with id=AA6, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.721A pdb=" N TYR C 390 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 385 through 386 Processing sheet with id=AA8, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.716A pdb=" N TYR D 390 " --> pdb=" O LEU D 732 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 3039 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: 7.08 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3787 1.33 - 1.45: 5727 1.45 - 1.57: 13062 1.57 - 1.70: 40 1.70 - 1.82: 224 Bond restraints: 22840 Sorted by residual: bond pdb=" O12 POV C 903 " pdb=" P POV C 903 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.57e+00 bond pdb=" O12 POV B 901 " pdb=" P POV B 901 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" O12 POV A 902 " pdb=" P POV A 902 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" O12 POV B 907 " pdb=" P POV B 907 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" O12 POV D 903 " pdb=" P POV D 903 " ideal model delta sigma weight residual 1.657 1.596 0.061 2.00e-02 2.50e+03 9.45e+00 ... (remaining 22835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 28457 1.07 - 2.14: 1751 2.14 - 3.21: 353 3.21 - 4.28: 124 4.28 - 5.34: 27 Bond angle restraints: 30712 Sorted by residual: angle pdb=" N ARG D 462 " pdb=" CA ARG D 462 " pdb=" C ARG D 462 " ideal model delta sigma weight residual 109.42 104.30 5.12 1.48e+00 4.57e-01 1.20e+01 angle pdb=" N CYS A 619 " pdb=" CA CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N CYS C 619 " pdb=" CA CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sigma weight residual 114.17 110.53 3.64 1.14e+00 7.69e-01 1.02e+01 angle pdb=" N CYS B 619 " pdb=" CA CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sigma weight residual 114.17 110.60 3.57 1.14e+00 7.69e-01 9.79e+00 angle pdb=" N ARG C 462 " pdb=" CA ARG C 462 " pdb=" C ARG C 462 " ideal model delta sigma weight residual 109.44 104.45 4.99 1.81e+00 3.05e-01 7.60e+00 ... (remaining 30707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 13653 34.83 - 69.66: 290 69.66 - 104.50: 40 104.50 - 139.33: 12 139.33 - 174.16: 17 Dihedral angle restraints: 14012 sinusoidal: 6308 harmonic: 7704 Sorted by residual: dihedral pdb=" CA TYR D 461 " pdb=" C TYR D 461 " pdb=" N ARG D 462 " pdb=" CA ARG D 462 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N ARG B 462 " pdb=" CA ARG B 462 " ideal model delta harmonic sigma weight residual 180.00 152.40 27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA TYR A 461 " pdb=" C TYR A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 14009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2483 0.035 - 0.071: 694 0.071 - 0.106: 160 0.106 - 0.142: 24 0.142 - 0.177: 11 Chirality restraints: 3372 Sorted by residual: chirality pdb=" C2 POV C 904 " pdb=" C1 POV C 904 " pdb=" C3 POV C 904 " pdb=" O21 POV C 904 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" C2 POV C 902 " pdb=" C1 POV C 902 " pdb=" C3 POV C 902 " pdb=" O21 POV C 902 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" C2 POV B 903 " pdb=" C1 POV B 903 " pdb=" C3 POV B 903 " pdb=" O21 POV B 903 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 3369 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 I8E B 906 " -0.012 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" C17 I8E B 906 " -0.017 2.00e-02 2.50e+03 pdb=" C3 I8E B 906 " 0.024 2.00e-02 2.50e+03 pdb=" C4 I8E B 906 " -0.016 2.00e-02 2.50e+03 pdb=" C5 I8E B 906 " -0.020 2.00e-02 2.50e+03 pdb=" C6 I8E B 906 " -0.013 2.00e-02 2.50e+03 pdb=" C7 I8E B 906 " -0.018 2.00e-02 2.50e+03 pdb=" C8 I8E B 906 " -0.019 2.00e-02 2.50e+03 pdb=" O15 I8E B 906 " 0.045 2.00e-02 2.50e+03 pdb=" O21 I8E B 906 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 I8E D 905 " 0.012 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" C17 I8E D 905 " 0.017 2.00e-02 2.50e+03 pdb=" C3 I8E D 905 " -0.023 2.00e-02 2.50e+03 pdb=" C4 I8E D 905 " 0.016 2.00e-02 2.50e+03 pdb=" C5 I8E D 905 " 0.020 2.00e-02 2.50e+03 pdb=" C6 I8E D 905 " 0.013 2.00e-02 2.50e+03 pdb=" C7 I8E D 905 " 0.018 2.00e-02 2.50e+03 pdb=" C8 I8E D 905 " 0.020 2.00e-02 2.50e+03 pdb=" O15 I8E D 905 " -0.045 2.00e-02 2.50e+03 pdb=" O21 I8E D 905 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 I8E C 905 " -0.012 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" C17 I8E C 905 " -0.017 2.00e-02 2.50e+03 pdb=" C3 I8E C 905 " 0.023 2.00e-02 2.50e+03 pdb=" C4 I8E C 905 " -0.016 2.00e-02 2.50e+03 pdb=" C5 I8E C 905 " -0.020 2.00e-02 2.50e+03 pdb=" C6 I8E C 905 " -0.013 2.00e-02 2.50e+03 pdb=" C7 I8E C 905 " -0.018 2.00e-02 2.50e+03 pdb=" C8 I8E C 905 " -0.020 2.00e-02 2.50e+03 pdb=" O15 I8E C 905 " 0.045 2.00e-02 2.50e+03 pdb=" O21 I8E C 905 " 0.047 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 209 2.58 - 3.16: 20293 3.16 - 3.74: 32289 3.74 - 4.32: 43520 4.32 - 4.90: 74451 Nonbonded interactions: 170762 Sorted by model distance: nonbonded pdb=" OG SER C 624 " pdb=" O13 POV C 904 " model vdw 2.001 3.040 nonbonded pdb=" OG SER B 624 " pdb=" O13 POV B 905 " model vdw 2.005 3.040 nonbonded pdb=" OG SER D 624 " pdb=" O13 POV D 904 " model vdw 2.009 3.040 nonbonded pdb=" OG SER A 444 " pdb=" O13 POV A 902 " model vdw 2.155 3.040 nonbonded pdb=" OG SER D 444 " pdb=" O13 POV D 903 " model vdw 2.161 3.040 ... (remaining 170757 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 59 through 751 or resid 901 through 903)) selection = (chain 'B' and (resid 59 through 751 or resid 901 through 903)) selection = (chain 'C' and (resid 59 through 751 or resid 901 through 903)) selection = (chain 'D' and (resid 59 through 751 or resid 901 through 903)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 48.720 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.100 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.004 0.062 22840 Z= 0.282 Angle : 0.628 5.344 30712 Z= 0.319 Chirality : 0.036 0.177 3372 Planarity : 0.004 0.082 3736 Dihedral : 16.488 174.158 8980 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 5.12 % Allowed : 9.47 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.18 (0.18), residues: 2596 helix: 0.88 (0.14), residues: 1552 sheet: -3.17 (0.59), residues: 64 loop : -3.52 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 521 HIS 0.006 0.001 HIS C 471 PHE 0.009 0.001 PHE B 316 TYR 0.013 0.001 TYR D 451 ARG 0.003 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 533 time to evaluate : 2.603 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: A 336 THR cc_start: 0.9010 (m) cc_final: 0.8779 (p) REVERT: A 347 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8026 (tt) REVERT: A 483 GLN cc_start: 0.7044 (tp40) cc_final: 0.6489 (tm-30) REVERT: A 485 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7653 (tm) REVERT: A 650 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5601 (m-10) REVERT: A 661 TYR cc_start: 0.8735 (t80) cc_final: 0.8337 (t80) REVERT: A 663 ILE cc_start: 0.9132 (tt) cc_final: 0.8914 (mt) REVERT: B 121 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8647 (mmmt) REVERT: B 336 THR cc_start: 0.9019 (m) cc_final: 0.8762 (p) REVERT: B 347 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7964 (tt) REVERT: B 358 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8640 (tptt) REVERT: B 483 GLN cc_start: 0.6919 (tp40) cc_final: 0.6400 (tm-30) REVERT: B 485 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7660 (tm) REVERT: B 650 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5611 (m-10) REVERT: B 661 TYR cc_start: 0.8738 (t80) cc_final: 0.8359 (t80) REVERT: B 663 ILE cc_start: 0.9144 (tt) cc_final: 0.8897 (mt) REVERT: C 121 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8658 (mmmt) REVERT: C 336 THR cc_start: 0.9015 (m) cc_final: 0.8753 (p) REVERT: C 347 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7939 (tt) REVERT: C 358 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8631 (tptt) REVERT: C 483 GLN cc_start: 0.7030 (tp40) cc_final: 0.6431 (tm-30) REVERT: C 485 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7645 (tm) REVERT: C 650 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: C 661 TYR cc_start: 0.8744 (t80) cc_final: 0.8354 (t80) REVERT: C 663 ILE cc_start: 0.9120 (tt) cc_final: 0.8875 (mt) REVERT: D 121 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8657 (mmmt) REVERT: D 336 THR cc_start: 0.9019 (m) cc_final: 0.8757 (p) REVERT: D 347 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7953 (tt) REVERT: D 358 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8642 (tptt) REVERT: D 483 GLN cc_start: 0.7032 (tp40) cc_final: 0.6420 (tm-30) REVERT: D 485 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7686 (tm) REVERT: D 650 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: D 661 TYR cc_start: 0.8760 (t80) cc_final: 0.8371 (t80) REVERT: D 663 ILE cc_start: 0.9153 (tt) cc_final: 0.8934 (mt) outliers start: 119 outliers final: 43 residues processed: 652 average time/residue: 0.4049 time to fit residues: 388.6857 Evaluate side-chains 371 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 227 GLN A 274 GLN A 346 GLN B 71 ASN B 227 GLN B 274 GLN B 346 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 274 GLN C 346 GLN D 71 ASN D 227 GLN D 274 GLN D 346 GLN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120246 restraints weight = 30640.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124216 restraints weight = 22554.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125941 restraints weight = 18258.148| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 22840 Z= 0.419 Angle : 0.833 9.969 30712 Z= 0.409 Chirality : 0.045 0.199 3372 Planarity : 0.005 0.076 3736 Dihedral : 19.099 179.523 3938 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.44 % Favored : 86.56 % Rotamer: Outliers : 6.50 % Allowed : 16.09 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.14 (0.17), residues: 2596 helix: 0.72 (0.13), residues: 1580 sheet: -2.61 (0.63), residues: 40 loop : -3.31 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 521 HIS 0.005 0.001 HIS C 256 PHE 0.022 0.002 PHE C 316 TYR 0.023 0.002 TYR D 461 ARG 0.005 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 355 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8323 (mtpt) REVERT: A 166 ASP cc_start: 0.7936 (t70) cc_final: 0.7644 (t0) REVERT: A 255 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8322 (mt0) REVERT: A 429 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7961 (mp) REVERT: A 483 GLN cc_start: 0.7473 (tp40) cc_final: 0.6265 (tm-30) REVERT: A 641 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7759 (p0) REVERT: A 650 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.5838 (m-10) REVERT: B 166 ASP cc_start: 0.7963 (t70) cc_final: 0.7662 (t0) REVERT: B 281 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7816 (mm) REVERT: B 358 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8884 (tttp) REVERT: B 483 GLN cc_start: 0.7433 (tp40) cc_final: 0.6253 (tm-30) REVERT: B 619 CYS cc_start: 0.1007 (OUTLIER) cc_final: 0.0664 (t) REVERT: B 641 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7685 (p0) REVERT: B 650 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.5846 (m-10) REVERT: C 166 ASP cc_start: 0.7954 (t70) cc_final: 0.7659 (t0) REVERT: C 358 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8898 (tttp) REVERT: C 483 GLN cc_start: 0.7434 (tp40) cc_final: 0.6243 (tm-30) REVERT: C 619 CYS cc_start: 0.1045 (OUTLIER) cc_final: 0.0717 (t) REVERT: C 641 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7741 (p0) REVERT: C 650 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5873 (m-10) REVERT: D 166 ASP cc_start: 0.7997 (t70) cc_final: 0.7609 (t0) REVERT: D 358 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8892 (tttp) REVERT: D 429 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7948 (mp) REVERT: D 464 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7118 (mtm180) REVERT: D 483 GLN cc_start: 0.7426 (tp40) cc_final: 0.6247 (tm-30) REVERT: D 619 CYS cc_start: 0.0956 (OUTLIER) cc_final: 0.0632 (t) REVERT: D 641 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7646 (p0) REVERT: D 650 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.5997 (m-10) outliers start: 151 outliers final: 91 residues processed: 484 average time/residue: 0.3480 time to fit residues: 261.5413 Evaluate side-chains 415 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 306 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 88 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 160 HIS A 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 160 HIS B 216 GLN B 417 HIS ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 160 HIS C 417 HIS D 71 ASN D 242 ASN D 417 HIS ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124534 restraints weight = 30659.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128565 restraints weight = 21937.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130277 restraints weight = 17360.078| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22840 Z= 0.252 Angle : 0.718 7.485 30712 Z= 0.356 Chirality : 0.041 0.169 3372 Planarity : 0.005 0.075 3736 Dihedral : 18.354 176.417 3916 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.90 % Favored : 87.94 % Rotamer: Outliers : 7.70 % Allowed : 17.69 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.07 (0.17), residues: 2596 helix: 0.86 (0.13), residues: 1556 sheet: -1.75 (0.68), residues: 40 loop : -3.37 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 521 HIS 0.004 0.001 HIS A 256 PHE 0.015 0.001 PHE C 316 TYR 0.013 0.001 TYR D 451 ARG 0.005 0.001 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 353 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8236 (mtpt) REVERT: A 166 ASP cc_start: 0.7923 (t70) cc_final: 0.7570 (t0) REVERT: A 268 LEU cc_start: 0.9349 (tm) cc_final: 0.9120 (tt) REVERT: A 429 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 479 MET cc_start: 0.3533 (tpt) cc_final: 0.3239 (tpt) REVERT: A 483 GLN cc_start: 0.7225 (tp40) cc_final: 0.5836 (tm-30) REVERT: A 541 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7780 (tp) REVERT: A 637 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5886 (pt) REVERT: A 650 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5649 (m-10) REVERT: B 121 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8165 (mtpt) REVERT: B 166 ASP cc_start: 0.7947 (t70) cc_final: 0.7580 (t0) REVERT: B 268 LEU cc_start: 0.9341 (tm) cc_final: 0.9125 (tt) REVERT: B 358 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8762 (tptt) REVERT: B 541 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7859 (tp) REVERT: B 637 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5853 (pt) REVERT: B 641 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7894 (p0) REVERT: B 650 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5790 (m-10) REVERT: B 725 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: B 749 LEU cc_start: 0.8212 (tp) cc_final: 0.8011 (tt) REVERT: C 166 ASP cc_start: 0.7975 (t70) cc_final: 0.7611 (t0) REVERT: C 268 LEU cc_start: 0.9352 (tm) cc_final: 0.9127 (tt) REVERT: C 358 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8780 (tptt) REVERT: C 541 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7896 (tp) REVERT: C 578 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7935 (mmp) REVERT: C 637 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.5843 (pt) REVERT: C 641 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7867 (p0) REVERT: C 650 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5720 (m-10) REVERT: D 268 LEU cc_start: 0.9356 (tm) cc_final: 0.9125 (tt) REVERT: D 358 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8778 (tptt) REVERT: D 429 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7847 (mp) REVERT: D 541 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7795 (tp) REVERT: D 578 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7923 (mmp) REVERT: D 637 ILE cc_start: 0.6227 (OUTLIER) cc_final: 0.5808 (pt) REVERT: D 641 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7871 (p0) REVERT: D 650 TYR cc_start: 0.6271 (OUTLIER) cc_final: 0.5784 (m-10) REVERT: D 725 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7118 (pm20) outliers start: 179 outliers final: 97 residues processed: 491 average time/residue: 0.3255 time to fit residues: 251.4720 Evaluate side-chains 430 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 309 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 286 GLN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 183 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 197 optimal weight: 0.0970 chunk 254 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 61 optimal weight: 0.0030 chunk 119 optimal weight: 1.9990 overall best weight: 2.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 160 HIS ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.163950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123952 restraints weight = 31012.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127826 restraints weight = 22224.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129482 restraints weight = 17761.033| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22840 Z= 0.254 Angle : 0.716 9.249 30712 Z= 0.351 Chirality : 0.041 0.166 3372 Planarity : 0.005 0.073 3736 Dihedral : 17.852 179.902 3916 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.44 % Favored : 87.40 % Rotamer: Outliers : 7.44 % Allowed : 18.37 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.98 (0.17), residues: 2596 helix: 0.98 (0.13), residues: 1536 sheet: -1.44 (0.68), residues: 40 loop : -3.37 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 493 HIS 0.005 0.001 HIS D 471 PHE 0.015 0.001 PHE D 316 TYR 0.014 0.002 TYR A 540 ARG 0.004 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 327 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8245 (mtpt) REVERT: A 166 ASP cc_start: 0.7935 (t70) cc_final: 0.7618 (t0) REVERT: A 268 LEU cc_start: 0.9298 (tm) cc_final: 0.9046 (tt) REVERT: A 429 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7821 (mp) REVERT: A 541 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7788 (tp) REVERT: A 637 ILE cc_start: 0.6282 (OUTLIER) cc_final: 0.5871 (pt) REVERT: A 641 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7906 (p0) REVERT: A 650 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5665 (m-10) REVERT: B 121 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8154 (mtpt) REVERT: B 166 ASP cc_start: 0.7933 (t70) cc_final: 0.7570 (t0) REVERT: B 268 LEU cc_start: 0.9305 (tm) cc_final: 0.9064 (tt) REVERT: B 358 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8860 (tttp) REVERT: B 541 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7796 (tp) REVERT: B 637 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5901 (pt) REVERT: B 650 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5798 (m-10) REVERT: B 725 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: B 749 LEU cc_start: 0.8171 (tp) cc_final: 0.7951 (tt) REVERT: C 121 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8089 (mtpt) REVERT: C 166 ASP cc_start: 0.7961 (t70) cc_final: 0.7598 (t0) REVERT: C 268 LEU cc_start: 0.9303 (tm) cc_final: 0.9057 (tt) REVERT: C 358 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8890 (tttp) REVERT: C 541 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7816 (tp) REVERT: C 578 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7932 (mmp) REVERT: C 637 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5914 (pt) REVERT: C 641 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7868 (p0) REVERT: C 650 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5793 (m-10) REVERT: D 268 LEU cc_start: 0.9309 (tm) cc_final: 0.9055 (tt) REVERT: D 358 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8880 (tttp) REVERT: D 429 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7812 (mp) REVERT: D 462 ARG cc_start: 0.7055 (mmt180) cc_final: 0.6301 (mmp80) REVERT: D 541 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7814 (tp) REVERT: D 578 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7924 (mmp) REVERT: D 637 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5909 (pt) REVERT: D 641 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7887 (p0) REVERT: D 650 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.5841 (m-10) REVERT: D 725 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7120 (pm20) outliers start: 173 outliers final: 108 residues processed: 469 average time/residue: 0.3368 time to fit residues: 253.0824 Evaluate side-chains 434 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 302 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 46 optimal weight: 0.1980 chunk 156 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.160991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120613 restraints weight = 30949.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124426 restraints weight = 22639.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126236 restraints weight = 18329.264| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22840 Z= 0.335 Angle : 0.751 17.112 30712 Z= 0.369 Chirality : 0.043 0.174 3372 Planarity : 0.004 0.072 3736 Dihedral : 17.265 172.080 3916 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.60 % Favored : 87.25 % Rotamer: Outliers : 7.57 % Allowed : 20.27 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.06 (0.17), residues: 2596 helix: 0.94 (0.13), residues: 1536 sheet: -1.55 (0.69), residues: 40 loop : -3.43 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 493 HIS 0.005 0.001 HIS C 256 PHE 0.018 0.002 PHE C 316 TYR 0.014 0.002 TYR B 451 ARG 0.004 0.001 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 321 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8275 (mtpt) REVERT: A 166 ASP cc_start: 0.7958 (t70) cc_final: 0.7661 (t0) REVERT: A 268 LEU cc_start: 0.9347 (tm) cc_final: 0.9088 (tt) REVERT: A 429 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7875 (mp) REVERT: A 541 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 637 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.5967 (pt) REVERT: A 641 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7976 (p0) REVERT: A 650 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.5742 (m-10) REVERT: B 121 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8103 (mtmt) REVERT: B 166 ASP cc_start: 0.7940 (t70) cc_final: 0.7632 (t0) REVERT: B 268 LEU cc_start: 0.9355 (tm) cc_final: 0.9108 (tt) REVERT: B 358 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8769 (tptt) REVERT: B 541 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7792 (tp) REVERT: B 637 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6021 (pt) REVERT: B 641 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7960 (p0) REVERT: B 650 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.5845 (m-10) REVERT: B 725 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: B 749 LEU cc_start: 0.8202 (tp) cc_final: 0.7971 (tt) REVERT: C 121 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8070 (mtpt) REVERT: C 166 ASP cc_start: 0.7943 (t70) cc_final: 0.7617 (t0) REVERT: C 268 LEU cc_start: 0.9351 (tm) cc_final: 0.9098 (tt) REVERT: C 358 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8872 (tttp) REVERT: C 541 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7809 (tp) REVERT: C 637 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6036 (pt) REVERT: C 641 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7918 (p0) REVERT: C 650 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5823 (m-10) REVERT: D 121 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8116 (mtpt) REVERT: D 268 LEU cc_start: 0.9333 (tm) cc_final: 0.9097 (tt) REVERT: D 358 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8761 (tptt) REVERT: D 429 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7881 (mp) REVERT: D 541 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7786 (tp) REVERT: D 637 ILE cc_start: 0.6420 (OUTLIER) cc_final: 0.6042 (pt) REVERT: D 641 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7897 (p0) REVERT: D 650 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.5877 (m-10) REVERT: D 725 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7184 (pm20) outliers start: 176 outliers final: 122 residues processed: 461 average time/residue: 0.3374 time to fit residues: 244.9414 Evaluate side-chains 443 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 298 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 73 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 190 optimal weight: 0.7980 chunk 252 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 242 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.163284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122897 restraints weight = 30503.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126527 restraints weight = 21759.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128463 restraints weight = 17447.923| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22840 Z= 0.236 Angle : 0.700 8.665 30712 Z= 0.346 Chirality : 0.041 0.160 3372 Planarity : 0.004 0.072 3736 Dihedral : 16.805 163.410 3916 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.94 % Favored : 87.98 % Rotamer: Outliers : 6.80 % Allowed : 21.90 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.96 (0.17), residues: 2596 helix: 1.02 (0.14), residues: 1536 sheet: -1.51 (0.73), residues: 40 loop : -3.39 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 493 HIS 0.005 0.001 HIS D 256 PHE 0.017 0.001 PHE C 316 TYR 0.016 0.001 TYR B 540 ARG 0.005 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 318 time to evaluate : 2.292 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: A 121 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8203 (mtpt) REVERT: A 166 ASP cc_start: 0.7966 (t70) cc_final: 0.7656 (t0) REVERT: A 268 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9053 (tt) REVERT: A 429 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 541 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7725 (tp) REVERT: A 637 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5814 (pt) REVERT: A 650 TYR cc_start: 0.6221 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: B 121 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8087 (mtpt) REVERT: B 166 ASP cc_start: 0.7955 (t70) cc_final: 0.7642 (t0) REVERT: B 268 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9050 (tt) REVERT: B 358 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8779 (tptt) REVERT: B 541 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7754 (tp) REVERT: B 637 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.5885 (pt) REVERT: B 650 TYR cc_start: 0.6159 (OUTLIER) cc_final: 0.5607 (m-10) REVERT: B 725 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: B 749 LEU cc_start: 0.8168 (tp) cc_final: 0.7934 (tt) REVERT: C 121 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8116 (mtmt) REVERT: C 166 ASP cc_start: 0.7968 (t70) cc_final: 0.7633 (t0) REVERT: C 268 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9062 (tt) REVERT: C 358 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8771 (tptt) REVERT: C 483 GLN cc_start: 0.7187 (tp40) cc_final: 0.5743 (tm-30) REVERT: C 541 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7757 (tp) REVERT: C 578 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7992 (mmp) REVERT: C 637 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5888 (pt) REVERT: C 650 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5742 (m-10) REVERT: D 121 LYS cc_start: 0.8663 (mmtm) cc_final: 0.8055 (mtpt) REVERT: D 268 LEU cc_start: 0.9293 (tm) cc_final: 0.9045 (tt) REVERT: D 358 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8769 (tptt) REVERT: D 429 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7801 (mp) REVERT: D 541 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7739 (tp) REVERT: D 578 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7953 (mmp) REVERT: D 618 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.4782 (m-30) REVERT: D 637 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5912 (pt) REVERT: D 650 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5763 (m-10) REVERT: D 725 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7908 (pm20) outliers start: 158 outliers final: 109 residues processed: 440 average time/residue: 0.3385 time to fit residues: 236.9192 Evaluate side-chains 436 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 302 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 192 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 71 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124511 restraints weight = 30761.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128286 restraints weight = 22259.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130050 restraints weight = 17880.836| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22840 Z= 0.209 Angle : 0.698 11.188 30712 Z= 0.345 Chirality : 0.041 0.179 3372 Planarity : 0.004 0.071 3736 Dihedral : 16.342 163.038 3916 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 6.20 % Allowed : 22.85 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.92 (0.17), residues: 2596 helix: 1.04 (0.14), residues: 1536 sheet: -1.36 (0.77), residues: 40 loop : -3.37 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 493 HIS 0.004 0.001 HIS C 256 PHE 0.018 0.001 PHE B 316 TYR 0.012 0.001 TYR D 622 ARG 0.002 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 328 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8193 (mtpt) REVERT: A 166 ASP cc_start: 0.7938 (t70) cc_final: 0.7630 (t0) REVERT: A 268 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9029 (tt) REVERT: A 429 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 637 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5648 (pt) REVERT: A 650 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5601 (m-10) REVERT: A 661 TYR cc_start: 0.8651 (t80) cc_final: 0.8241 (t80) REVERT: B 121 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8016 (mtpt) REVERT: B 166 ASP cc_start: 0.7925 (t70) cc_final: 0.7609 (t0) REVERT: B 268 LEU cc_start: 0.9279 (tm) cc_final: 0.9031 (tt) REVERT: B 358 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8790 (tptt) REVERT: B 637 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5724 (pt) REVERT: B 650 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5593 (m-10) REVERT: B 661 TYR cc_start: 0.8659 (t80) cc_final: 0.8242 (t80) REVERT: B 749 LEU cc_start: 0.8157 (tp) cc_final: 0.7924 (tt) REVERT: C 121 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8057 (mtmt) REVERT: C 166 ASP cc_start: 0.7949 (t70) cc_final: 0.7628 (t0) REVERT: C 268 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9028 (tt) REVERT: C 358 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8793 (tptt) REVERT: C 578 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7927 (mmp) REVERT: C 618 ASP cc_start: 0.6105 (OUTLIER) cc_final: 0.4693 (m-30) REVERT: C 637 ILE cc_start: 0.6154 (OUTLIER) cc_final: 0.5715 (pt) REVERT: C 650 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.5740 (m-10) REVERT: C 661 TYR cc_start: 0.8659 (t80) cc_final: 0.8244 (t80) REVERT: D 121 LYS cc_start: 0.8643 (mmtm) cc_final: 0.8066 (mtmt) REVERT: D 268 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9037 (tt) REVERT: D 358 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8776 (tptt) REVERT: D 429 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7865 (mp) REVERT: D 637 ILE cc_start: 0.6176 (OUTLIER) cc_final: 0.5752 (pt) REVERT: D 650 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5620 (m-10) REVERT: D 661 TYR cc_start: 0.8660 (t80) cc_final: 0.8238 (t80) REVERT: D 725 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7889 (pm20) outliers start: 144 outliers final: 111 residues processed: 441 average time/residue: 0.3168 time to fit residues: 224.9319 Evaluate side-chains 431 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 301 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 204 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 585 HIS A 646 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** C 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 HIS D 410 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS ** D 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121921 restraints weight = 30702.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125313 restraints weight = 22224.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127191 restraints weight = 17992.840| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22840 Z= 0.295 Angle : 0.732 17.409 30712 Z= 0.361 Chirality : 0.042 0.170 3372 Planarity : 0.004 0.070 3736 Dihedral : 16.167 160.589 3914 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 6.67 % Allowed : 22.85 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.04 (0.17), residues: 2596 helix: 0.93 (0.14), residues: 1548 sheet: -1.58 (0.74), residues: 40 loop : -3.43 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 493 HIS 0.011 0.001 HIS A 585 PHE 0.021 0.001 PHE A 316 TYR 0.019 0.002 TYR A 540 ARG 0.007 0.001 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 293 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8170 (mtpt) REVERT: A 166 ASP cc_start: 0.7933 (t70) cc_final: 0.7643 (t0) REVERT: A 207 GLU cc_start: 0.7988 (pm20) cc_final: 0.7712 (mm-30) REVERT: A 429 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7754 (mp) REVERT: A 637 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.5963 (pt) REVERT: A 650 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: B 121 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8046 (mtpt) REVERT: B 268 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9057 (tt) REVERT: B 358 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8787 (tptt) REVERT: B 618 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.4662 (m-30) REVERT: B 637 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6061 (pt) REVERT: B 650 TYR cc_start: 0.6211 (OUTLIER) cc_final: 0.5640 (m-10) REVERT: B 690 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7279 (mtt180) REVERT: B 749 LEU cc_start: 0.8238 (tp) cc_final: 0.7979 (tt) REVERT: C 121 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8025 (mtmt) REVERT: C 166 ASP cc_start: 0.7967 (t70) cc_final: 0.7655 (t0) REVERT: C 358 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8880 (tttp) REVERT: C 618 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.4684 (m-30) REVERT: C 637 ILE cc_start: 0.6411 (OUTLIER) cc_final: 0.6016 (pt) REVERT: C 650 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5710 (m-10) REVERT: C 690 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7293 (mtt180) REVERT: D 121 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8064 (mtmt) REVERT: D 358 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8853 (tttp) REVERT: D 429 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7891 (mp) REVERT: D 637 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.6037 (pt) REVERT: D 641 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7302 (p0) REVERT: D 650 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5569 (m-10) REVERT: D 725 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7926 (pm20) outliers start: 155 outliers final: 121 residues processed: 423 average time/residue: 0.3205 time to fit residues: 217.1508 Evaluate side-chains 424 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 285 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 114 optimal weight: 0.0050 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126876 restraints weight = 30344.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130797 restraints weight = 21383.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132660 restraints weight = 16985.303| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22840 Z= 0.170 Angle : 0.698 16.969 30712 Z= 0.342 Chirality : 0.040 0.209 3372 Planarity : 0.004 0.070 3736 Dihedral : 15.679 161.814 3914 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 5.64 % Allowed : 24.53 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.90 (0.17), residues: 2596 helix: 1.12 (0.14), residues: 1536 sheet: -1.44 (0.77), residues: 40 loop : -3.47 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 493 HIS 0.005 0.001 HIS D 417 PHE 0.017 0.001 PHE B 316 TYR 0.009 0.001 TYR A 661 ARG 0.014 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 335 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8050 (mtpt) REVERT: A 166 ASP cc_start: 0.7938 (t70) cc_final: 0.7627 (t0) REVERT: A 429 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 637 ILE cc_start: 0.5819 (OUTLIER) cc_final: 0.5429 (pt) REVERT: A 650 TYR cc_start: 0.6182 (OUTLIER) cc_final: 0.5468 (m-10) REVERT: A 661 TYR cc_start: 0.8595 (t80) cc_final: 0.8292 (t80) REVERT: B 121 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8015 (mtpt) REVERT: B 135 LEU cc_start: 0.7528 (mm) cc_final: 0.7246 (mm) REVERT: B 268 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9061 (tt) REVERT: B 618 ASP cc_start: 0.5781 (OUTLIER) cc_final: 0.4567 (m-30) REVERT: B 637 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5498 (pt) REVERT: B 650 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5555 (m-10) REVERT: B 661 TYR cc_start: 0.8604 (t80) cc_final: 0.8319 (t80) REVERT: B 749 LEU cc_start: 0.8149 (tp) cc_final: 0.7922 (tt) REVERT: C 618 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.4611 (m-30) REVERT: C 637 ILE cc_start: 0.5833 (OUTLIER) cc_final: 0.5461 (pt) REVERT: C 650 TYR cc_start: 0.6101 (OUTLIER) cc_final: 0.5466 (m-10) REVERT: C 661 TYR cc_start: 0.8603 (t80) cc_final: 0.8317 (t80) REVERT: D 135 LEU cc_start: 0.7491 (mm) cc_final: 0.7288 (mm) REVERT: D 429 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7790 (mp) REVERT: D 637 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5487 (pt) REVERT: D 650 TYR cc_start: 0.6073 (OUTLIER) cc_final: 0.5448 (m-10) REVERT: D 661 TYR cc_start: 0.8607 (t80) cc_final: 0.8317 (t80) REVERT: D 690 ARG cc_start: 0.7495 (mtp85) cc_final: 0.7181 (mtt180) outliers start: 131 outliers final: 96 residues processed: 441 average time/residue: 0.3202 time to fit residues: 226.3367 Evaluate side-chains 402 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 293 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 232 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 130 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 646 GLN ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129133 restraints weight = 30384.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133096 restraints weight = 21746.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134976 restraints weight = 17220.275| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22840 Z= 0.169 Angle : 0.715 17.611 30712 Z= 0.352 Chirality : 0.040 0.170 3372 Planarity : 0.004 0.071 3736 Dihedral : 15.122 161.373 3888 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 4.82 % Allowed : 25.22 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.79 (0.17), residues: 2596 helix: 1.20 (0.14), residues: 1540 sheet: -3.23 (0.52), residues: 96 loop : -3.28 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 493 HIS 0.005 0.001 HIS A 417 PHE 0.017 0.001 PHE A 316 TYR 0.007 0.001 TYR A 208 ARG 0.016 0.000 ARG C 690 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 319 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8059 (mtpt) REVERT: A 637 ILE cc_start: 0.5608 (pp) cc_final: 0.5165 (pt) REVERT: A 650 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.5339 (m-10) REVERT: A 657 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 661 TYR cc_start: 0.8559 (t80) cc_final: 0.8216 (t80) REVERT: B 121 LYS cc_start: 0.8783 (mmmt) cc_final: 0.7997 (mtpt) REVERT: B 135 LEU cc_start: 0.7325 (mm) cc_final: 0.7070 (mm) REVERT: B 268 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9041 (tt) REVERT: B 618 ASP cc_start: 0.5772 (OUTLIER) cc_final: 0.4533 (m-30) REVERT: B 637 ILE cc_start: 0.5679 (pp) cc_final: 0.5238 (pt) REVERT: B 650 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.5442 (m-10) REVERT: B 657 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 661 TYR cc_start: 0.8544 (t80) cc_final: 0.8204 (t80) REVERT: B 749 LEU cc_start: 0.8116 (tp) cc_final: 0.7899 (tt) REVERT: C 268 LEU cc_start: 0.9189 (tp) cc_final: 0.8896 (tt) REVERT: C 618 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.4465 (m-30) REVERT: C 637 ILE cc_start: 0.5642 (pp) cc_final: 0.5207 (pt) REVERT: C 650 TYR cc_start: 0.6013 (OUTLIER) cc_final: 0.5415 (m-10) REVERT: C 657 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7841 (mp) REVERT: C 661 TYR cc_start: 0.8544 (t80) cc_final: 0.8205 (t80) REVERT: D 268 LEU cc_start: 0.9218 (tp) cc_final: 0.8958 (tt) REVERT: D 637 ILE cc_start: 0.5668 (pp) cc_final: 0.5234 (pt) REVERT: D 650 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5336 (m-10) REVERT: D 657 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7794 (mp) REVERT: D 661 TYR cc_start: 0.8554 (t80) cc_final: 0.8215 (t80) outliers start: 112 outliers final: 85 residues processed: 418 average time/residue: 0.3111 time to fit residues: 208.7864 Evaluate side-chains 394 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 298 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 258 optimal weight: 8.9990 chunk 233 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 646 GLN ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 646 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126693 restraints weight = 30535.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130756 restraints weight = 21460.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132536 restraints weight = 16951.005| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22840 Z= 0.199 Angle : 0.726 17.371 30712 Z= 0.355 Chirality : 0.041 0.185 3372 Planarity : 0.004 0.069 3736 Dihedral : 14.870 159.943 3888 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 4.69 % Allowed : 24.87 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.75 (0.17), residues: 2596 helix: 1.22 (0.14), residues: 1544 sheet: -2.44 (0.66), residues: 64 loop : -3.36 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 493 HIS 0.004 0.001 HIS C 256 PHE 0.017 0.001 PHE A 436 TYR 0.009 0.001 TYR D 451 ARG 0.008 0.000 ARG D 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7078.62 seconds wall clock time: 129 minutes 26.70 seconds (7766.70 seconds total)