Starting phenix.real_space_refine on Wed Jun 25 03:12:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s91_40234/06_2025/8s91_40234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s91_40234/06_2025/8s91_40234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s91_40234/06_2025/8s91_40234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s91_40234/06_2025/8s91_40234.map" model { file = "/net/cci-nas-00/data/ceres_data/8s91_40234/06_2025/8s91_40234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s91_40234/06_2025/8s91_40234.cif" } resolution = 4.3 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= -0.001 sd= 0.028 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 12 5.49 5 Mg 6 5.21 5 S 177 5.16 5 C 18309 2.51 5 N 4980 2.21 5 O 5535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29019 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4703 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 29, 'TRANS': 572} Chain breaks: 5 Chain: "B" Number of atoms: 4703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4703 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 29, 'TRANS': 572} Chain breaks: 5 Chain: "C" Number of atoms: 4703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4703 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 29, 'TRANS': 572} Chain breaks: 5 Chain: "D" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4914 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 22, 'TRANS': 598} Chain breaks: 4 Chain: "E" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4914 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 22, 'TRANS': 598} Chain breaks: 4 Chain: "F" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4914 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 22, 'TRANS': 598} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.78, per 1000 atoms: 0.58 Number of scatterers: 29019 At special positions: 0 Unit cell: (153.18, 153.18, 127.65, 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 177 16.00 P 12 15.00 Mg 6 11.99 O 5535 8.00 N 4980 7.00 C 18309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.53 Conformation dependent library (CDL) restraints added in 3.4 seconds 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6936 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 28 sheets defined 40.6% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.585A pdb=" N TRP A 78 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 79' Processing helix chain 'A' and resid 91 through 106 removed outlier: 4.280A pdb=" N LYS A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.589A pdb=" N ILE A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.618A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 148 through 175 removed outlier: 3.996A pdb=" N THR A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 401 through 408 removed outlier: 3.584A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.531A pdb=" N LYS A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.516A pdb=" N ALA A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.605A pdb=" N LEU A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.735A pdb=" N ARG A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 582 through 587' Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 662 through 674 removed outlier: 3.705A pdb=" N LYS A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 671 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 701 removed outlier: 3.512A pdb=" N ALA A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.542A pdb=" N GLU A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.832A pdb=" N ILE A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.607A pdb=" N TYR A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 753' Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.551A pdb=" N TRP B 78 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS B 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 75 through 79' Processing helix chain 'B' and resid 91 through 106 removed outlier: 4.270A pdb=" N LYS B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.646A pdb=" N ILE B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 150 through 175 removed outlier: 3.711A pdb=" N CYS B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.654A pdb=" N LEU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.519A pdb=" N LYS B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.633A pdb=" N ALA B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 537 removed outlier: 3.507A pdb=" N GLU B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 4.053A pdb=" N ARG B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 587' Processing helix chain 'B' and resid 599 through 612 removed outlier: 3.558A pdb=" N HIS B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 674 removed outlier: 3.795A pdb=" N GLY B 671 " --> pdb=" O ARG B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 701 removed outlier: 3.972A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 removed outlier: 3.534A pdb=" N GLU B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 removed outlier: 3.516A pdb=" N ASP B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.527A pdb=" N TYR B 752 " --> pdb=" O MET B 748 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 753' Processing helix chain 'C' and resid 75 through 79 removed outlier: 3.527A pdb=" N TRP C 78 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS C 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 79' Processing helix chain 'C' and resid 91 through 106 removed outlier: 4.265A pdb=" N LYS C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 118 removed outlier: 3.753A pdb=" N ILE C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 148 through 175 removed outlier: 4.060A pdb=" N THR C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 153 " --> pdb=" O PRO C 149 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 398 Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.606A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 430 removed outlier: 3.630A pdb=" N LYS C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 536 Processing helix chain 'C' and resid 600 through 612 Processing helix chain 'C' and resid 662 through 675 removed outlier: 3.707A pdb=" N LYS C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY C 671 " --> pdb=" O ARG C 667 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 672 " --> pdb=" O LYS C 668 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 675 " --> pdb=" O GLY C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 701 removed outlier: 3.501A pdb=" N ALA C 686 " --> pdb=" O SER C 682 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG C 687 " --> pdb=" O THR C 683 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 723 removed outlier: 3.717A pdb=" N GLU C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 745 removed outlier: 3.977A pdb=" N ILE C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 743 " --> pdb=" O ASP C 739 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 745 " --> pdb=" O VAL C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 4.446A pdb=" N SER C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 21 removed outlier: 3.804A pdb=" N VAL D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D 7 " --> pdb=" O SER D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 30 removed outlier: 3.892A pdb=" N ILE D 25 " --> pdb=" O HIS D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 52 through 59 removed outlier: 4.231A pdb=" N GLU D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 83 removed outlier: 4.041A pdb=" N THR D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.608A pdb=" N TYR D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 310 removed outlier: 3.994A pdb=" N ARG D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.878A pdb=" N GLY D 330 " --> pdb=" O MET D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 removed outlier: 3.850A pdb=" N LYS D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.985A pdb=" N LEU D 385 " --> pdb=" O THR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 3.787A pdb=" N ASP D 407 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.549A pdb=" N GLU D 432 " --> pdb=" O HIS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 468 through 473 Processing helix chain 'D' and resid 496 through 507 Processing helix chain 'D' and resid 520 through 531 Processing helix chain 'D' and resid 539 through 555 removed outlier: 3.969A pdb=" N ASN D 543 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN D 544 " --> pdb=" O ASP D 540 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN D 555 " --> pdb=" O GLN D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 581 removed outlier: 3.581A pdb=" N GLU D 570 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 604 removed outlier: 3.609A pdb=" N ALA D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 598 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 599 " --> pdb=" O THR D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 639 removed outlier: 3.883A pdb=" N GLN D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 639 " --> pdb=" O ILE D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 654 removed outlier: 3.732A pdb=" N LEU D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 646 " --> pdb=" O GLN D 642 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 654 " --> pdb=" O ARG D 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.798A pdb=" N VAL E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR E 7 " --> pdb=" O SER E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 removed outlier: 3.736A pdb=" N ILE E 25 " --> pdb=" O HIS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 51 through 59 removed outlier: 4.297A pdb=" N GLY E 55 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E 56 " --> pdb=" O MET E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 83 removed outlier: 3.918A pdb=" N THR E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.785A pdb=" N GLN E 162 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR E 163 " --> pdb=" O PHE E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 163' Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 298 through 310 removed outlier: 4.627A pdb=" N GLY E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG E 303 " --> pdb=" O PRO E 299 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 330 removed outlier: 3.920A pdb=" N GLY E 330 " --> pdb=" O MET E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 369 removed outlier: 3.686A pdb=" N LYS E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 368 " --> pdb=" O TYR E 364 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.873A pdb=" N LEU E 385 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.694A pdb=" N ASP E 407 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 426 Processing helix chain 'E' and resid 427 through 433 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 468 through 473 Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.790A pdb=" N SER E 481 " --> pdb=" O PRO E 478 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG E 482 " --> pdb=" O LEU E 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 478 through 482' Processing helix chain 'E' and resid 496 through 507 Processing helix chain 'E' and resid 520 through 531 Processing helix chain 'E' and resid 539 through 544 removed outlier: 3.771A pdb=" N ASN E 543 " --> pdb=" O SER E 539 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 539 through 544' Processing helix chain 'E' and resid 545 through 555 removed outlier: 5.072A pdb=" N GLN E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN E 555 " --> pdb=" O GLN E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 573 removed outlier: 3.693A pdb=" N GLU E 570 " --> pdb=" O ILE E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 580 Processing helix chain 'E' and resid 589 through 604 removed outlier: 3.831A pdb=" N ALA E 593 " --> pdb=" O THR E 589 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER E 598 " --> pdb=" O ILE E 594 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 599 " --> pdb=" O THR E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 639 removed outlier: 3.898A pdb=" N GLN E 627 " --> pdb=" O ASN E 623 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS E 638 " --> pdb=" O LEU E 634 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 654 removed outlier: 3.754A pdb=" N LEU E 645 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER E 646 " --> pdb=" O GLN E 642 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU E 647 " --> pdb=" O SER E 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.854A pdb=" N VAL F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR F 7 " --> pdb=" O SER F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.902A pdb=" N ILE F 25 " --> pdb=" O HIS F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 51 through 59 removed outlier: 4.498A pdb=" N GLY F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 83 removed outlier: 4.002A pdb=" N THR F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 282 through 295 Processing helix chain 'F' and resid 298 through 310 removed outlier: 4.493A pdb=" N GLY F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG F 303 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 330 removed outlier: 3.514A pdb=" N LYS F 321 " --> pdb=" O MET F 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY F 330 " --> pdb=" O MET F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 369 removed outlier: 3.557A pdb=" N PHE F 361 " --> pdb=" O GLY F 357 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 368 " --> pdb=" O TYR F 364 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR F 369 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.854A pdb=" N LEU F 385 " --> pdb=" O THR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 removed outlier: 3.670A pdb=" N ASP F 407 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 426 Processing helix chain 'F' and resid 427 through 433 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 468 through 473 removed outlier: 3.625A pdb=" N ASN F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 508 removed outlier: 3.601A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 531 Processing helix chain 'F' and resid 539 through 554 removed outlier: 3.913A pdb=" N ASN F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN F 544 " --> pdb=" O ASP F 540 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU F 546 " --> pdb=" O GLY F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 581 removed outlier: 3.561A pdb=" N GLU F 570 " --> pdb=" O ILE F 566 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG F 574 " --> pdb=" O GLU F 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 581 " --> pdb=" O GLU F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 604 removed outlier: 3.539A pdb=" N ALA F 593 " --> pdb=" O THR F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 639 removed outlier: 4.052A pdb=" N GLN F 627 " --> pdb=" O ASN F 623 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU F 637 " --> pdb=" O GLU F 633 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS F 638 " --> pdb=" O LEU F 634 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 654 removed outlier: 3.732A pdb=" N LEU F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER F 646 " --> pdb=" O GLN F 642 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU F 647 " --> pdb=" O SER F 643 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 124 removed outlier: 8.075A pdb=" N HIS A 195 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL A 123 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A 197 " --> pdb=" O VAL A 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 225 removed outlier: 3.577A pdb=" N THR A 224 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 294 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 311 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N THR A 310 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ILE A 357 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 312 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 359 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU A 314 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N SER A 361 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A 332 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 362 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR A 330 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 333 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 219 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA4, first strand: chain 'A' and resid 517 through 518 removed outlier: 3.527A pdb=" N ALA A 559 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 450 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ALA A 560 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL A 452 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.465A pdb=" N ARG B 197 " --> pdb=" O VAL B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 219 through 223 removed outlier: 3.590A pdb=" N ILE B 219 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 331 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 330 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE B 362 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR B 332 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N THR B 310 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N ILE B 357 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU B 312 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 359 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU B 314 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER B 361 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 311 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AA9, first strand: chain 'B' and resid 517 through 518 removed outlier: 3.507A pdb=" N ALA B 559 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 450 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ALA B 560 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 452 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AB2, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.510A pdb=" N ARG C 197 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 219 through 220 removed outlier: 3.954A pdb=" N ILE C 219 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 333 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 332 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR C 310 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE C 357 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU C 312 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA C 359 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU C 314 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER C 361 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB5, first strand: chain 'C' and resid 352 through 353 Processing sheet with id=AB6, first strand: chain 'C' and resid 477 through 478 removed outlier: 7.176A pdb=" N VAL C 477 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 559 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE C 450 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ALA C 560 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 452 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AB8, first strand: chain 'D' and resid 39 through 43 removed outlier: 3.526A pdb=" N VAL D 40 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 240 removed outlier: 6.719A pdb=" N LYS D 203 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR D 133 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU D 201 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D 200 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 224 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 202 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N SER D 219 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N LEU D 263 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LYS D 221 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ALA D 265 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE D 223 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 247 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 372 through 375 removed outlier: 3.840A pdb=" N ASP D 414 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 452 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS D 411 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 454 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 456 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU D 348 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR D 457 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU D 350 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU D 349 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU D 489 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 351 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 435 through 438 removed outlier: 3.743A pdb=" N LEU D 447 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 438 " --> pdb=" O CYS D 445 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 38 through 43 removed outlier: 3.578A pdb=" N HIS E 97 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 40 " --> pdb=" O HIS E 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 126 through 133 removed outlier: 6.644A pdb=" N LYS E 203 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR E 133 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU E 201 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN E 200 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 224 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 202 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N SER E 219 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 9.685A pdb=" N LEU E 263 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA E 265 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE E 223 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR E 267 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N GLU E 225 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 12.276A pdb=" N GLN E 269 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR E 241 " --> pdb=" O ASN E 266 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE E 268 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR E 239 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY E 128 " --> pdb=" O LEU E 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 372 through 374 removed outlier: 6.874A pdb=" N VAL E 373 " --> pdb=" O CYS E 412 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP E 414 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 452 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU E 454 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 456 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY E 352 " --> pdb=" O THR E 457 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU E 349 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU E 489 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL E 351 " --> pdb=" O LEU E 489 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 435 through 438 removed outlier: 3.806A pdb=" N LEU E 447 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 438 " --> pdb=" O CYS E 445 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 41 through 43 Processing sheet with id=AC8, first strand: chain 'F' and resid 123 through 133 removed outlier: 6.725A pdb=" N LYS F 203 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR F 133 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU F 201 " --> pdb=" O THR F 133 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN F 200 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 224 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N SER F 219 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N LEU F 263 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS F 221 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA F 265 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE F 223 " --> pdb=" O ALA F 265 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 126 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY F 242 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 372 through 374 removed outlier: 6.951A pdb=" N VAL F 373 " --> pdb=" O CYS F 412 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASP F 414 " --> pdb=" O VAL F 373 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR F 452 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS F 411 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 454 " --> pdb=" O CYS F 411 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 456 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY F 352 " --> pdb=" O THR F 457 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU F 349 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU F 489 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 351 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 435 through 438 removed outlier: 3.671A pdb=" N LEU F 447 " --> pdb=" O ILE F 436 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 438 " --> pdb=" O CYS F 445 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2595 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.15 Time building geometry restraints manager: 7.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9580 1.34 - 1.46: 6085 1.46 - 1.58: 13558 1.58 - 1.70: 18 1.70 - 1.82: 264 Bond restraints: 29505 Sorted by residual: bond pdb=" N ASP E 226 " pdb=" CA ASP E 226 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.84e+00 bond pdb=" CB GLN E 82 " pdb=" CG GLN E 82 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB GLU E 31 " pdb=" CG GLU E 31 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CA LEU F 480 " pdb=" CB LEU F 480 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.31e-02 5.83e+03 1.13e+00 bond pdb=" CA VAL B 210 " pdb=" CB VAL B 210 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.06e+00 ... (remaining 29500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 39582 3.21 - 6.42: 323 6.42 - 9.62: 20 9.62 - 12.83: 4 12.83 - 16.04: 1 Bond angle restraints: 39930 Sorted by residual: angle pdb=" C ALA C 560 " pdb=" N ASN C 561 " pdb=" CA ASN C 561 " ideal model delta sigma weight residual 122.31 138.35 -16.04 2.34e+00 1.83e-01 4.70e+01 angle pdb=" C LEU F 518 " pdb=" N TRP F 519 " pdb=" CA TRP F 519 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.63e+01 angle pdb=" C LEU E 518 " pdb=" CA LEU E 518 " pdb=" CB LEU E 518 " ideal model delta sigma weight residual 116.54 109.64 6.90 1.15e+00 7.56e-01 3.60e+01 angle pdb=" C LEU D 518 " pdb=" N TRP D 519 " pdb=" CA TRP D 519 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" C LEU E 518 " pdb=" N TRP E 519 " pdb=" CA TRP E 519 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 ... (remaining 39925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 17489 32.01 - 64.02: 492 64.02 - 96.03: 64 96.03 - 128.03: 11 128.03 - 160.04: 7 Dihedral angle restraints: 18063 sinusoidal: 7365 harmonic: 10698 Sorted by residual: dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 100.05 -160.04 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 99.35 -159.35 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP C2001 " pdb=" O5' ADP C2001 " pdb=" PA ADP C2001 " pdb=" O2A ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 97.08 -157.08 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 18060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3434 0.043 - 0.086: 892 0.086 - 0.129: 270 0.129 - 0.172: 26 0.172 - 0.215: 4 Chirality restraints: 4626 Sorted by residual: chirality pdb=" CB ILE F 486 " pdb=" CA ILE F 486 " pdb=" CG1 ILE F 486 " pdb=" CG2 ILE F 486 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLU B 202 " pdb=" N GLU B 202 " pdb=" C GLU B 202 " pdb=" CB GLU B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CB THR E 338 " pdb=" CA THR E 338 " pdb=" OG1 THR E 338 " pdb=" CG2 THR E 338 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 4623 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 518 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C LEU E 518 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU E 518 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP E 519 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 518 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C LEU F 518 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU F 518 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP F 519 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 266 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO B 267 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " 0.041 5.00e-02 4.00e+02 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 197 2.55 - 3.14: 22344 3.14 - 3.73: 41622 3.73 - 4.31: 51829 4.31 - 4.90: 86673 Nonbonded interactions: 202665 Sorted by model distance: nonbonded pdb=" O1B ADP E2001 " pdb="MG MG E2002 " model vdw 1.964 2.170 nonbonded pdb=" O1B ADP D2001 " pdb="MG MG D2002 " model vdw 1.999 2.170 nonbonded pdb=" O2B ADP D2001 " pdb="MG MG D2002 " model vdw 2.057 2.170 nonbonded pdb=" O THR E 46 " pdb=" OG1 THR E 50 " model vdw 2.083 3.040 nonbonded pdb=" OG SER C 461 " pdb="MG MG C2002 " model vdw 2.104 2.170 ... (remaining 202660 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.090 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: 1.260 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 60.210 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.003 0.043 29505 Z= 0.130 Angle : 0.711 16.038 39930 Z= 0.373 Chirality : 0.042 0.215 4626 Planarity : 0.005 0.073 5091 Dihedral : 15.789 160.042 11127 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.41 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.14), residues: 3603 helix: 0.56 (0.16), residues: 1269 sheet: -0.96 (0.24), residues: 474 loop : -2.39 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 292 HIS 0.010 0.001 HIS F 37 PHE 0.022 0.001 PHE B 102 TYR 0.023 0.001 TYR B 391 ARG 0.010 0.001 ARG D 559 Details of bonding type rmsd hydrogen bonds : bond 0.20258 ( 907) hydrogen bonds : angle 6.67544 ( 2595) covalent geometry : bond 0.00255 (29505) covalent geometry : angle 0.71129 (39930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 TYR cc_start: 0.8559 (t80) cc_final: 0.8316 (t80) REVERT: B 113 ASP cc_start: 0.6985 (t70) cc_final: 0.6730 (t70) REVERT: B 258 TYR cc_start: 0.7986 (t80) cc_final: 0.7683 (t80) REVERT: C 151 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8079 (ttmm) REVERT: D 52 MET cc_start: 0.7995 (pmm) cc_final: 0.7638 (tmm) REVERT: D 134 SER cc_start: 0.7477 (t) cc_final: 0.7036 (p) REVERT: D 220 MET cc_start: 0.8190 (tpp) cc_final: 0.7965 (mmm) REVERT: D 524 MET cc_start: 0.7181 (tpp) cc_final: 0.6915 (mmt) REVERT: E 114 ILE cc_start: 0.8025 (mm) cc_final: 0.7543 (tp) REVERT: F 51 ASN cc_start: 0.8957 (t0) cc_final: 0.8520 (t0) REVERT: F 60 MET cc_start: 0.8116 (ttt) cc_final: 0.7647 (ttt) REVERT: F 146 MET cc_start: 0.5218 (pmm) cc_final: 0.4720 (ppp) REVERT: F 651 ARG cc_start: 0.8375 (ttt180) cc_final: 0.7839 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.3700 time to fit residues: 357.6927 Evaluate side-chains 425 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 213 ASN A 394 GLN A 462 GLN A 600 HIS A 608 HIS B 213 ASN B 394 GLN B 449 HIS B 603 HIS B 608 HIS C 213 ASN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 209 GLN D 433 GLN D 434 GLN E 5 GLN E 433 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.164829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127795 restraints weight = 49882.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127707 restraints weight = 40625.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128577 restraints weight = 34762.899| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29505 Z= 0.134 Angle : 0.640 7.568 39930 Z= 0.319 Chirality : 0.043 0.182 4626 Planarity : 0.005 0.069 5091 Dihedral : 9.278 164.914 4032 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.83 % Favored : 89.73 % Rotamer: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.14), residues: 3603 helix: 0.76 (0.16), residues: 1275 sheet: -1.21 (0.23), residues: 519 loop : -2.44 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 292 HIS 0.007 0.001 HIS F 37 PHE 0.021 0.001 PHE E 13 TYR 0.018 0.001 TYR E 199 ARG 0.005 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 907) hydrogen bonds : angle 4.81652 ( 2595) covalent geometry : bond 0.00301 (29505) covalent geometry : angle 0.63952 (39930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 593 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8546 (mt) cc_final: 0.8226 (mp) REVERT: A 391 TYR cc_start: 0.8495 (t80) cc_final: 0.8184 (t80) REVERT: A 523 MET cc_start: 0.4868 (mtt) cc_final: 0.4625 (mtt) REVERT: A 538 SER cc_start: 0.8414 (m) cc_final: 0.8001 (p) REVERT: A 539 ILE cc_start: 0.8469 (tt) cc_final: 0.8159 (tt) REVERT: A 657 THR cc_start: 0.7900 (m) cc_final: 0.7646 (t) REVERT: B 113 ASP cc_start: 0.7112 (t70) cc_final: 0.6874 (t70) REVERT: B 258 TYR cc_start: 0.8218 (t80) cc_final: 0.7936 (t80) REVERT: B 352 MET cc_start: 0.6790 (mmm) cc_final: 0.6574 (tpp) REVERT: B 390 LEU cc_start: 0.9543 (mp) cc_final: 0.9293 (mp) REVERT: C 113 ASP cc_start: 0.7138 (t70) cc_final: 0.6657 (t70) REVERT: C 151 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8163 (ttmm) REVERT: D 52 MET cc_start: 0.8058 (pmm) cc_final: 0.7605 (tmm) REVERT: D 134 SER cc_start: 0.7898 (t) cc_final: 0.7516 (p) REVERT: D 287 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7658 (tm-30) REVERT: D 317 MET cc_start: 0.6861 (mmm) cc_final: 0.6344 (mmp) REVERT: D 651 ARG cc_start: 0.8235 (tmm-80) cc_final: 0.7880 (tmm-80) REVERT: E 438 VAL cc_start: 0.7713 (m) cc_final: 0.7509 (p) REVERT: E 651 ARG cc_start: 0.8099 (tmm-80) cc_final: 0.7819 (tmm-80) REVERT: F 32 ARG cc_start: 0.7411 (tpt90) cc_final: 0.7124 (tpt90) REVERT: F 51 ASN cc_start: 0.8742 (t0) cc_final: 0.8274 (t0) REVERT: F 146 MET cc_start: 0.5254 (pmm) cc_final: 0.4780 (ppp) REVERT: F 166 PHE cc_start: 0.8220 (m-80) cc_final: 0.7226 (m-80) outliers start: 3 outliers final: 0 residues processed: 594 average time/residue: 0.3741 time to fit residues: 364.9913 Evaluate side-chains 428 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 246 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 188 optimal weight: 0.9980 chunk 338 optimal weight: 0.4980 chunk 178 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN B 394 GLN C 171 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 162 GLN D 434 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123549 restraints weight = 49115.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124230 restraints weight = 37822.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125483 restraints weight = 31296.676| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29505 Z= 0.144 Angle : 0.659 7.780 39930 Z= 0.328 Chirality : 0.043 0.192 4626 Planarity : 0.005 0.066 5091 Dihedral : 8.872 167.143 4032 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.19 % Favored : 89.40 % Rotamer: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.14), residues: 3603 helix: 0.66 (0.16), residues: 1284 sheet: -1.24 (0.23), residues: 519 loop : -2.37 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 519 HIS 0.009 0.001 HIS E 37 PHE 0.032 0.002 PHE E 13 TYR 0.018 0.001 TYR E 199 ARG 0.007 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 907) hydrogen bonds : angle 4.49765 ( 2595) covalent geometry : bond 0.00327 (29505) covalent geometry : angle 0.65898 (39930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 621 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8871 (mt) cc_final: 0.8670 (mp) REVERT: A 231 ILE cc_start: 0.8590 (pt) cc_final: 0.8243 (pt) REVERT: A 315 LEU cc_start: 0.8619 (mt) cc_final: 0.8254 (mp) REVERT: A 387 LEU cc_start: 0.8884 (mt) cc_final: 0.8641 (pt) REVERT: A 391 TYR cc_start: 0.8571 (t80) cc_final: 0.8264 (t80) REVERT: A 538 SER cc_start: 0.8636 (m) cc_final: 0.8154 (p) REVERT: A 539 ILE cc_start: 0.8517 (tt) cc_final: 0.8244 (tt) REVERT: B 113 ASP cc_start: 0.7149 (t70) cc_final: 0.6912 (t70) REVERT: B 258 TYR cc_start: 0.8285 (t80) cc_final: 0.8017 (t80) REVERT: B 390 LEU cc_start: 0.9573 (mp) cc_final: 0.9323 (mp) REVERT: C 136 ASN cc_start: 0.9095 (m110) cc_final: 0.8820 (m-40) REVERT: C 151 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8250 (ttmm) REVERT: D 51 ASN cc_start: 0.8691 (m-40) cc_final: 0.8442 (t0) REVERT: D 134 SER cc_start: 0.8392 (t) cc_final: 0.7830 (p) REVERT: D 287 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7640 (tm-30) REVERT: D 317 MET cc_start: 0.6619 (mmm) cc_final: 0.5838 (mmp) REVERT: D 349 LEU cc_start: 0.7718 (tp) cc_final: 0.7292 (tp) REVERT: D 521 MET cc_start: 0.8236 (ppp) cc_final: 0.8007 (ppp) REVERT: D 651 ARG cc_start: 0.8264 (tmm-80) cc_final: 0.7868 (tmm-80) REVERT: E 112 GLU cc_start: 0.8488 (mp0) cc_final: 0.7871 (tp30) REVERT: E 349 LEU cc_start: 0.7849 (tp) cc_final: 0.7567 (tp) REVERT: E 438 VAL cc_start: 0.7891 (m) cc_final: 0.7660 (p) REVERT: E 651 ARG cc_start: 0.8083 (tmm-80) cc_final: 0.7758 (tmm-80) REVERT: F 51 ASN cc_start: 0.8590 (t0) cc_final: 0.8121 (t0) REVERT: F 146 MET cc_start: 0.5434 (pmm) cc_final: 0.4912 (ppp) REVERT: F 349 LEU cc_start: 0.8085 (tp) cc_final: 0.7679 (tp) outliers start: 3 outliers final: 0 residues processed: 622 average time/residue: 0.3802 time to fit residues: 382.1518 Evaluate side-chains 423 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 265 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 345 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 82 optimal weight: 0.0770 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 394 GLN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN C 106 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN E 560 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125046 restraints weight = 48667.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126327 restraints weight = 35795.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127170 restraints weight = 29218.657| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29505 Z= 0.110 Angle : 0.628 8.190 39930 Z= 0.310 Chirality : 0.042 0.177 4626 Planarity : 0.004 0.066 5091 Dihedral : 8.629 173.736 4032 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.74 % Favored : 89.81 % Rotamer: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.14), residues: 3603 helix: 0.71 (0.15), residues: 1302 sheet: -1.16 (0.23), residues: 519 loop : -2.36 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 519 HIS 0.008 0.001 HIS E 37 PHE 0.024 0.001 PHE D 13 TYR 0.014 0.001 TYR B 391 ARG 0.005 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 907) hydrogen bonds : angle 4.23284 ( 2595) covalent geometry : bond 0.00241 (29505) covalent geometry : angle 0.62781 (39930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 605 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.7957 (tpp) cc_final: 0.7708 (tpp) REVERT: A 387 LEU cc_start: 0.8884 (mt) cc_final: 0.8635 (pt) REVERT: A 391 TYR cc_start: 0.8660 (t80) cc_final: 0.8361 (t80) REVERT: A 538 SER cc_start: 0.8676 (m) cc_final: 0.8134 (p) REVERT: A 539 ILE cc_start: 0.8442 (tt) cc_final: 0.8199 (tt) REVERT: B 113 ASP cc_start: 0.7150 (t70) cc_final: 0.6906 (t70) REVERT: B 289 GLN cc_start: 0.8228 (pp30) cc_final: 0.7532 (pp30) REVERT: C 113 ASP cc_start: 0.6821 (t70) cc_final: 0.6579 (t70) REVERT: C 151 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8314 (ttmm) REVERT: D 51 ASN cc_start: 0.8578 (m-40) cc_final: 0.8315 (t0) REVERT: D 134 SER cc_start: 0.8306 (t) cc_final: 0.7770 (p) REVERT: D 220 MET cc_start: 0.8229 (tpp) cc_final: 0.7872 (tpt) REVERT: D 287 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 317 MET cc_start: 0.6496 (mmm) cc_final: 0.6074 (mmp) REVERT: D 349 LEU cc_start: 0.7733 (tp) cc_final: 0.7391 (tp) REVERT: D 521 MET cc_start: 0.8144 (ppp) cc_final: 0.7882 (ppp) REVERT: D 651 ARG cc_start: 0.8277 (tmm-80) cc_final: 0.7844 (tmm-80) REVERT: E 112 GLU cc_start: 0.8528 (mp0) cc_final: 0.7877 (tp30) REVERT: E 166 PHE cc_start: 0.8492 (m-10) cc_final: 0.8255 (m-10) REVERT: E 289 GLU cc_start: 0.8922 (mp0) cc_final: 0.8176 (tp30) REVERT: E 438 VAL cc_start: 0.7929 (m) cc_final: 0.7713 (p) REVERT: E 651 ARG cc_start: 0.8136 (tmm-80) cc_final: 0.7821 (tmm-80) REVERT: F 51 ASN cc_start: 0.8546 (t0) cc_final: 0.8105 (t0) REVERT: F 146 MET cc_start: 0.5488 (pmm) cc_final: 0.5091 (ppp) REVERT: F 254 ASP cc_start: 0.9159 (m-30) cc_final: 0.8950 (m-30) REVERT: F 295 TYR cc_start: 0.8225 (m-80) cc_final: 0.6867 (m-80) REVERT: F 349 LEU cc_start: 0.8071 (tp) cc_final: 0.7702 (tp) REVERT: F 651 ARG cc_start: 0.8308 (ttt180) cc_final: 0.7887 (tmm-80) outliers start: 2 outliers final: 0 residues processed: 606 average time/residue: 0.4191 time to fit residues: 413.9705 Evaluate side-chains 426 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 144 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 251 optimal weight: 1.9990 chunk 339 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 282 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN B 394 GLN B 600 HIS C 171 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 434 GLN E 59 ASN E 448 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 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 = 0.3938 r_free = 0.3938 target = 0.156937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118310 restraints weight = 49135.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119041 restraints weight = 37034.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119584 restraints weight = 31562.868| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29505 Z= 0.186 Angle : 0.721 10.101 39930 Z= 0.357 Chirality : 0.045 0.200 4626 Planarity : 0.005 0.065 5091 Dihedral : 8.670 162.817 4032 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.05 % Favored : 88.54 % Rotamer: Outliers : 0.12 % Allowed : 3.51 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.14), residues: 3603 helix: 0.55 (0.15), residues: 1293 sheet: -1.42 (0.21), residues: 591 loop : -2.41 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 519 HIS 0.006 0.001 HIS C 449 PHE 0.033 0.002 PHE D 13 TYR 0.022 0.002 TYR E 199 ARG 0.008 0.001 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 907) hydrogen bonds : angle 4.54972 ( 2595) covalent geometry : bond 0.00433 (29505) covalent geometry : angle 0.72106 (39930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 572 time to evaluate : 4.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9086 (mt) cc_final: 0.8829 (pt) REVERT: A 391 TYR cc_start: 0.8482 (t80) cc_final: 0.8191 (t80) REVERT: A 538 SER cc_start: 0.8871 (m) cc_final: 0.8303 (p) REVERT: A 539 ILE cc_start: 0.8646 (tt) cc_final: 0.8421 (tt) REVERT: A 748 MET cc_start: 0.5579 (mmp) cc_final: 0.5343 (tpp) REVERT: B 113 ASP cc_start: 0.7157 (t70) cc_final: 0.6945 (t70) REVERT: B 258 TYR cc_start: 0.8446 (t80) cc_final: 0.8184 (t80) REVERT: C 105 ARG cc_start: 0.8461 (mtm110) cc_final: 0.8232 (mtm110) REVERT: C 151 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8353 (ttmm) REVERT: D 134 SER cc_start: 0.8753 (t) cc_final: 0.8231 (p) REVERT: D 287 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 317 MET cc_start: 0.6536 (mmm) cc_final: 0.6241 (mmp) REVERT: D 438 VAL cc_start: 0.7609 (m) cc_final: 0.7405 (p) REVERT: D 521 MET cc_start: 0.8154 (ppp) cc_final: 0.7860 (ppp) REVERT: D 651 ARG cc_start: 0.8205 (tmm-80) cc_final: 0.7814 (tmm-80) REVERT: E 112 GLU cc_start: 0.8516 (mp0) cc_final: 0.7835 (tp30) REVERT: E 349 LEU cc_start: 0.8207 (tp) cc_final: 0.7853 (tp) REVERT: E 629 GLN cc_start: 0.8736 (tt0) cc_final: 0.7752 (tm-30) REVERT: E 651 ARG cc_start: 0.8170 (tmm-80) cc_final: 0.7841 (tmm-80) REVERT: F 1 MET cc_start: 0.4003 (mmt) cc_final: 0.3697 (mmp) REVERT: F 51 ASN cc_start: 0.8584 (t0) cc_final: 0.8056 (t0) REVERT: F 146 MET cc_start: 0.5746 (pmm) cc_final: 0.5121 (ppp) REVERT: F 295 TYR cc_start: 0.8314 (m-80) cc_final: 0.6794 (m-80) REVERT: F 349 LEU cc_start: 0.8306 (tp) cc_final: 0.7882 (tp) REVERT: F 493 LYS cc_start: 0.8057 (mppt) cc_final: 0.7787 (tptp) outliers start: 4 outliers final: 0 residues processed: 575 average time/residue: 0.5409 time to fit residues: 513.2769 Evaluate side-chains 410 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 260 optimal weight: 0.0970 chunk 253 optimal weight: 7.9990 chunk 350 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 364 optimal weight: 1.9990 chunk 338 optimal weight: 0.7980 chunk 305 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 536 GLN B 106 HIS B 600 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 434 GLN E 59 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125309 restraints weight = 45781.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128438 restraints weight = 32715.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129454 restraints weight = 26208.882| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29505 Z= 0.118 Angle : 0.660 9.375 39930 Z= 0.324 Chirality : 0.043 0.188 4626 Planarity : 0.004 0.065 5091 Dihedral : 8.503 169.827 4032 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.77 % Favored : 89.81 % Rotamer: Outliers : 0.09 % Allowed : 2.27 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.14), residues: 3603 helix: 0.73 (0.15), residues: 1287 sheet: -1.37 (0.21), residues: 621 loop : -2.37 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 519 HIS 0.005 0.001 HIS E 37 PHE 0.025 0.001 PHE D 13 TYR 0.015 0.001 TYR A 391 ARG 0.006 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 907) hydrogen bonds : angle 4.26258 ( 2595) covalent geometry : bond 0.00264 (29505) covalent geometry : angle 0.65952 (39930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 582 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8883 (mt) cc_final: 0.8655 (pt) REVERT: A 538 SER cc_start: 0.8806 (m) cc_final: 0.8263 (p) REVERT: A 539 ILE cc_start: 0.8603 (tt) cc_final: 0.8387 (tt) REVERT: A 748 MET cc_start: 0.5319 (mmp) cc_final: 0.5113 (tpp) REVERT: B 289 GLN cc_start: 0.8533 (pp30) cc_final: 0.7829 (pp30) REVERT: B 391 TYR cc_start: 0.7916 (t80) cc_final: 0.7706 (t80) REVERT: C 101 LYS cc_start: 0.9226 (mttt) cc_final: 0.8703 (tppt) REVERT: C 113 ASP cc_start: 0.6830 (t70) cc_final: 0.6592 (t70) REVERT: C 151 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8289 (ttmm) REVERT: C 748 MET cc_start: 0.6126 (mmm) cc_final: 0.5863 (mmm) REVERT: D 134 SER cc_start: 0.8641 (t) cc_final: 0.8072 (p) REVERT: D 287 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7789 (tm-30) REVERT: D 317 MET cc_start: 0.6496 (mmm) cc_final: 0.6273 (mmp) REVERT: D 349 LEU cc_start: 0.7948 (tp) cc_final: 0.7503 (tp) REVERT: D 519 TRP cc_start: 0.4867 (m-10) cc_final: 0.4500 (m-10) REVERT: D 521 MET cc_start: 0.8045 (ppp) cc_final: 0.7810 (ppp) REVERT: D 651 ARG cc_start: 0.8245 (tmm-80) cc_final: 0.7851 (tmm-80) REVERT: E 112 GLU cc_start: 0.8426 (mp0) cc_final: 0.7880 (tp30) REVERT: E 349 LEU cc_start: 0.8151 (tp) cc_final: 0.7878 (tp) REVERT: E 629 GLN cc_start: 0.8580 (tt0) cc_final: 0.7547 (tm-30) REVERT: E 651 ARG cc_start: 0.8062 (tmm-80) cc_final: 0.7730 (tmm-80) REVERT: E 654 ARG cc_start: 0.7725 (ptp90) cc_final: 0.7296 (ptp-170) REVERT: F 1 MET cc_start: 0.3877 (mmt) cc_final: 0.3427 (mmp) REVERT: F 51 ASN cc_start: 0.8510 (t0) cc_final: 0.8135 (t0) REVERT: F 60 MET cc_start: 0.7797 (tmm) cc_final: 0.6477 (tmm) REVERT: F 146 MET cc_start: 0.5321 (pmm) cc_final: 0.4839 (ppp) REVERT: F 254 ASP cc_start: 0.9191 (m-30) cc_final: 0.8985 (m-30) REVERT: F 295 TYR cc_start: 0.8328 (m-80) cc_final: 0.6935 (m-80) REVERT: F 349 LEU cc_start: 0.8215 (tp) cc_final: 0.7825 (tp) REVERT: F 651 ARG cc_start: 0.8292 (ttt180) cc_final: 0.7850 (tmm-80) outliers start: 3 outliers final: 0 residues processed: 584 average time/residue: 0.3828 time to fit residues: 359.3670 Evaluate side-chains 415 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 249 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 364 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 600 HIS C 171 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 434 GLN E 59 ASN E 246 GLN E 448 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.157446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119146 restraints weight = 48687.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.119717 restraints weight = 38658.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120731 restraints weight = 32562.121| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29505 Z= 0.158 Angle : 0.690 9.916 39930 Z= 0.342 Chirality : 0.044 0.185 4626 Planarity : 0.005 0.063 5091 Dihedral : 8.466 166.124 4032 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.21 % Favored : 88.32 % Rotamer: Outliers : 0.12 % Allowed : 1.77 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.14), residues: 3603 helix: 0.69 (0.15), residues: 1278 sheet: -1.52 (0.21), residues: 606 loop : -2.37 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 292 HIS 0.006 0.001 HIS C 449 PHE 0.029 0.002 PHE D 13 TYR 0.023 0.001 TYR B 391 ARG 0.007 0.000 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 907) hydrogen bonds : angle 4.37359 ( 2595) covalent geometry : bond 0.00367 (29505) covalent geometry : angle 0.68967 (39930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 560 time to evaluate : 4.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8710 (mt) cc_final: 0.8315 (mp) REVERT: A 387 LEU cc_start: 0.8912 (mt) cc_final: 0.8669 (pt) REVERT: A 538 SER cc_start: 0.8904 (m) cc_final: 0.8394 (p) REVERT: B 113 ASP cc_start: 0.7027 (t70) cc_final: 0.6519 (t70) REVERT: B 258 TYR cc_start: 0.8489 (t80) cc_final: 0.8262 (t80) REVERT: B 289 GLN cc_start: 0.8370 (pp30) cc_final: 0.7570 (pp30) REVERT: B 731 GLU cc_start: 0.7387 (tp30) cc_final: 0.7102 (tp30) REVERT: C 101 LYS cc_start: 0.9249 (mttt) cc_final: 0.8982 (mttp) REVERT: C 105 ARG cc_start: 0.8297 (mtm110) cc_final: 0.7850 (mtm110) REVERT: C 151 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8402 (ttmm) REVERT: D 45 MET cc_start: 0.7875 (mmp) cc_final: 0.7597 (tpp) REVERT: D 134 SER cc_start: 0.8791 (t) cc_final: 0.8268 (p) REVERT: D 201 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7911 (tt0) REVERT: D 240 ILE cc_start: 0.9224 (mt) cc_final: 0.8990 (mt) REVERT: D 287 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 317 MET cc_start: 0.6560 (mmm) cc_final: 0.5969 (mmp) REVERT: D 637 GLU cc_start: 0.7936 (tt0) cc_final: 0.7187 (tm-30) REVERT: D 651 ARG cc_start: 0.8186 (tmm-80) cc_final: 0.7766 (tmm-80) REVERT: E 92 MET cc_start: 0.7498 (ttm) cc_final: 0.7015 (tpt) REVERT: E 112 GLU cc_start: 0.8495 (mp0) cc_final: 0.7840 (tp30) REVERT: E 114 ILE cc_start: 0.8301 (mm) cc_final: 0.7893 (tp) REVERT: E 166 PHE cc_start: 0.8533 (m-10) cc_final: 0.8321 (m-10) REVERT: E 349 LEU cc_start: 0.8206 (tp) cc_final: 0.7961 (tp) REVERT: E 629 GLN cc_start: 0.8779 (tt0) cc_final: 0.7671 (tm-30) REVERT: E 651 ARG cc_start: 0.8033 (tmm-80) cc_final: 0.7702 (tmm-80) REVERT: F 1 MET cc_start: 0.3718 (mmt) cc_final: 0.3368 (mmp) REVERT: F 51 ASN cc_start: 0.8543 (t0) cc_final: 0.8053 (t0) REVERT: F 146 MET cc_start: 0.6050 (pmm) cc_final: 0.5361 (ppp) REVERT: F 166 PHE cc_start: 0.8585 (m-10) cc_final: 0.8326 (m-10) REVERT: F 254 ASP cc_start: 0.9249 (m-30) cc_final: 0.9039 (m-30) REVERT: F 295 TYR cc_start: 0.8502 (m-80) cc_final: 0.7098 (m-80) REVERT: F 349 LEU cc_start: 0.8368 (tp) cc_final: 0.7982 (tp) outliers start: 4 outliers final: 0 residues processed: 563 average time/residue: 0.4647 time to fit residues: 424.9824 Evaluate side-chains 400 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 121 optimal weight: 3.9990 chunk 299 optimal weight: 0.0270 chunk 294 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 171 optimal weight: 0.4980 chunk 297 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 339 optimal weight: 10.0000 chunk 324 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 394 GLN B 213 ASN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 600 HIS C 480 ASN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN E 59 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 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 = 0.3930 r_free = 0.3930 target = 0.157876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123505 restraints weight = 47227.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124121 restraints weight = 41500.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125230 restraints weight = 35357.240| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29505 Z= 0.153 Angle : 0.705 10.412 39930 Z= 0.348 Chirality : 0.045 0.201 4626 Planarity : 0.005 0.063 5091 Dihedral : 8.436 166.410 4032 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.82 % Favored : 88.76 % Rotamer: Outliers : 0.09 % Allowed : 1.21 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.14), residues: 3603 helix: 0.63 (0.15), residues: 1278 sheet: -1.45 (0.21), residues: 603 loop : -2.40 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 292 HIS 0.004 0.001 HIS C 449 PHE 0.027 0.002 PHE D 13 TYR 0.020 0.001 TYR E 199 ARG 0.010 0.000 ARG E 654 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 907) hydrogen bonds : angle 4.42049 ( 2595) covalent geometry : bond 0.00354 (29505) covalent geometry : angle 0.70476 (39930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 551 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8753 (mt) cc_final: 0.8428 (mp) REVERT: A 390 LEU cc_start: 0.9457 (mt) cc_final: 0.9222 (mt) REVERT: A 538 SER cc_start: 0.8861 (m) cc_final: 0.8392 (p) REVERT: A 576 ASN cc_start: 0.8224 (m110) cc_final: 0.7748 (t0) REVERT: B 289 GLN cc_start: 0.8454 (pp30) cc_final: 0.7665 (pp30) REVERT: B 536 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8415 (mm-40) REVERT: B 748 MET cc_start: 0.5925 (mmm) cc_final: 0.5656 (mmm) REVERT: C 101 LYS cc_start: 0.9237 (mttt) cc_final: 0.8705 (tppt) REVERT: C 105 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7689 (mtm110) REVERT: C 151 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8449 (ttmm) REVERT: D 45 MET cc_start: 0.7700 (mmp) cc_final: 0.7418 (tpp) REVERT: D 134 SER cc_start: 0.8848 (t) cc_final: 0.8391 (p) REVERT: D 201 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7985 (tt0) REVERT: D 240 ILE cc_start: 0.9196 (mt) cc_final: 0.8986 (mt) REVERT: D 245 MET cc_start: 0.7976 (mmm) cc_final: 0.7693 (mmm) REVERT: D 287 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 637 GLU cc_start: 0.7915 (tt0) cc_final: 0.7193 (tm-30) REVERT: D 651 ARG cc_start: 0.8319 (tmm-80) cc_final: 0.7884 (tmm-80) REVERT: E 92 MET cc_start: 0.7651 (ttm) cc_final: 0.7200 (tpt) REVERT: E 112 GLU cc_start: 0.8382 (mp0) cc_final: 0.7842 (tp30) REVERT: E 114 ILE cc_start: 0.8356 (mm) cc_final: 0.8075 (tp) REVERT: E 349 LEU cc_start: 0.8149 (tp) cc_final: 0.7906 (tp) REVERT: E 629 GLN cc_start: 0.8689 (tt0) cc_final: 0.7423 (tm-30) REVERT: F 1 MET cc_start: 0.3799 (mmt) cc_final: 0.3437 (mmp) REVERT: F 51 ASN cc_start: 0.8597 (t0) cc_final: 0.8189 (t0) REVERT: F 146 MET cc_start: 0.5740 (pmm) cc_final: 0.5279 (ppp) REVERT: F 295 TYR cc_start: 0.8577 (m-80) cc_final: 0.7447 (m-80) REVERT: F 349 LEU cc_start: 0.8440 (tp) cc_final: 0.8118 (tp) outliers start: 3 outliers final: 0 residues processed: 554 average time/residue: 0.3894 time to fit residues: 348.5942 Evaluate side-chains 411 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 0.0870 chunk 183 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 289 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 295 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS C 171 HIS C 480 ASN D 5 GLN D 59 ASN E 59 ASN E 448 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.159575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122660 restraints weight = 50046.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122079 restraints weight = 44281.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123330 restraints weight = 39393.633| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29505 Z= 0.118 Angle : 0.687 10.057 39930 Z= 0.338 Chirality : 0.044 0.196 4626 Planarity : 0.004 0.062 5091 Dihedral : 8.278 171.630 4032 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.35 % Favored : 89.23 % Rotamer: Outliers : 0.09 % Allowed : 0.84 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.14), residues: 3603 helix: 0.68 (0.15), residues: 1278 sheet: -1.31 (0.21), residues: 597 loop : -2.38 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 292 HIS 0.003 0.001 HIS E 37 PHE 0.052 0.002 PHE D 61 TYR 0.019 0.001 TYR A 567 ARG 0.007 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 907) hydrogen bonds : angle 4.32508 ( 2595) covalent geometry : bond 0.00259 (29505) covalent geometry : angle 0.68743 (39930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 567 time to evaluate : 7.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 GLN cc_start: 0.8561 (mp10) cc_final: 0.8190 (mp10) REVERT: A 538 SER cc_start: 0.8919 (m) cc_final: 0.8493 (p) REVERT: A 539 ILE cc_start: 0.8597 (tt) cc_final: 0.8278 (tt) REVERT: A 576 ASN cc_start: 0.8273 (m110) cc_final: 0.7523 (t0) REVERT: B 289 GLN cc_start: 0.8509 (pp30) cc_final: 0.7739 (pp30) REVERT: B 536 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8513 (mm-40) REVERT: C 101 LYS cc_start: 0.9238 (mttt) cc_final: 0.8672 (tppt) REVERT: C 151 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8474 (ttmm) REVERT: C 748 MET cc_start: 0.6219 (mmm) cc_final: 0.5794 (mmm) REVERT: D 31 GLU cc_start: 0.7801 (tp30) cc_final: 0.7405 (tp30) REVERT: D 60 MET cc_start: 0.8048 (tmm) cc_final: 0.7274 (tmm) REVERT: D 134 SER cc_start: 0.8799 (t) cc_final: 0.8332 (p) REVERT: D 201 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8060 (tt0) REVERT: D 240 ILE cc_start: 0.9161 (mt) cc_final: 0.8943 (mt) REVERT: D 245 MET cc_start: 0.8021 (mmm) cc_final: 0.7790 (mmm) REVERT: D 287 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 637 GLU cc_start: 0.7909 (tt0) cc_final: 0.7158 (tm-30) REVERT: D 651 ARG cc_start: 0.8278 (tmm-80) cc_final: 0.7826 (tmm-80) REVERT: E 45 MET cc_start: 0.7109 (mmp) cc_final: 0.6293 (mmp) REVERT: E 92 MET cc_start: 0.7674 (ttm) cc_final: 0.7179 (tpt) REVERT: E 114 ILE cc_start: 0.8353 (mm) cc_final: 0.8096 (tp) REVERT: E 629 GLN cc_start: 0.8707 (tt0) cc_final: 0.7463 (tm-30) REVERT: E 654 ARG cc_start: 0.7968 (ptp-170) cc_final: 0.7720 (ptp-170) REVERT: F 1 MET cc_start: 0.3542 (mmt) cc_final: 0.3221 (mmp) REVERT: F 51 ASN cc_start: 0.8455 (t0) cc_final: 0.8076 (t0) REVERT: F 146 MET cc_start: 0.6015 (pmm) cc_final: 0.5367 (ppp) REVERT: F 254 ASP cc_start: 0.9186 (m-30) cc_final: 0.8981 (m-30) REVERT: F 295 TYR cc_start: 0.8593 (m-80) cc_final: 0.7237 (m-80) REVERT: F 349 LEU cc_start: 0.8413 (tp) cc_final: 0.8104 (tp) outliers start: 3 outliers final: 0 residues processed: 569 average time/residue: 0.4981 time to fit residues: 465.7152 Evaluate side-chains 406 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 195 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 chunk 126 optimal weight: 0.0970 chunk 309 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 359 optimal weight: 6.9990 chunk 364 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 209 ASN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 434 GLN E 59 ASN E 246 GLN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118262 restraints weight = 47536.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119873 restraints weight = 38200.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121561 restraints weight = 30599.106| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29505 Z= 0.173 Angle : 0.742 11.191 39930 Z= 0.367 Chirality : 0.046 0.192 4626 Planarity : 0.005 0.062 5091 Dihedral : 8.321 165.388 4032 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.93 % Favored : 87.65 % Rotamer: Outliers : 0.06 % Allowed : 0.43 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.14), residues: 3603 helix: 0.53 (0.15), residues: 1278 sheet: -1.41 (0.21), residues: 606 loop : -2.41 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 292 HIS 0.004 0.001 HIS C 449 PHE 0.032 0.002 PHE E 13 TYR 0.023 0.002 TYR B 391 ARG 0.009 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 907) hydrogen bonds : angle 4.55965 ( 2595) covalent geometry : bond 0.00394 (29505) covalent geometry : angle 0.74181 (39930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 539 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7293 (ttp80) cc_final: 0.7073 (ttp80) REVERT: B 289 GLN cc_start: 0.8389 (pp30) cc_final: 0.7494 (pp30) REVERT: B 536 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8529 (mm-40) REVERT: C 101 LYS cc_start: 0.9236 (mttt) cc_final: 0.8700 (tppt) REVERT: C 151 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8601 (tttp) REVERT: D 31 GLU cc_start: 0.7904 (tp30) cc_final: 0.7521 (tp30) REVERT: D 94 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8772 (mm-40) REVERT: D 134 SER cc_start: 0.8990 (t) cc_final: 0.8559 (p) REVERT: D 201 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8102 (tt0) REVERT: D 287 GLU cc_start: 0.8674 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 448 ASN cc_start: 0.7946 (m110) cc_final: 0.7665 (m-40) REVERT: D 637 GLU cc_start: 0.7829 (tt0) cc_final: 0.7092 (tm-30) REVERT: D 651 ARG cc_start: 0.8282 (tmm-80) cc_final: 0.7844 (tmm-80) REVERT: E 92 MET cc_start: 0.7734 (ttm) cc_final: 0.7219 (tpt) REVERT: E 112 GLU cc_start: 0.8023 (pm20) cc_final: 0.7806 (tp30) REVERT: E 349 LEU cc_start: 0.8302 (tp) cc_final: 0.8074 (tp) REVERT: E 629 GLN cc_start: 0.8720 (tt0) cc_final: 0.8380 (tp40) REVERT: E 654 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.7628 (ptp-170) REVERT: F 1 MET cc_start: 0.3818 (mmt) cc_final: 0.3459 (mmp) REVERT: F 51 ASN cc_start: 0.8501 (t0) cc_final: 0.8111 (t0) REVERT: F 146 MET cc_start: 0.6085 (pmm) cc_final: 0.5488 (ppp) REVERT: F 295 TYR cc_start: 0.8725 (m-80) cc_final: 0.7655 (m-80) REVERT: F 349 LEU cc_start: 0.8544 (tp) cc_final: 0.8244 (tp) REVERT: F 552 MET cc_start: 0.8221 (tpp) cc_final: 0.7879 (tpt) REVERT: F 614 ASN cc_start: 0.7457 (m-40) cc_final: 0.7125 (m-40) outliers start: 2 outliers final: 1 residues processed: 541 average time/residue: 0.3818 time to fit residues: 339.9132 Evaluate side-chains 387 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 261 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 256 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 136 ASN ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS D 434 GLN E 59 ASN E 448 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.152769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111829 restraints weight = 50264.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113900 restraints weight = 39680.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114737 restraints weight = 34367.737| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29505 Z= 0.208 Angle : 0.784 13.421 39930 Z= 0.388 Chirality : 0.047 0.281 4626 Planarity : 0.005 0.062 5091 Dihedral : 8.439 157.710 4032 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.96 % Favored : 87.59 % Rotamer: Outliers : 0.06 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.89 (0.14), residues: 3603 helix: 0.37 (0.15), residues: 1275 sheet: -1.51 (0.21), residues: 606 loop : -2.48 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 292 HIS 0.006 0.001 HIS C 449 PHE 0.031 0.003 PHE E 69 TYR 0.027 0.002 TYR E 199 ARG 0.010 0.001 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 907) hydrogen bonds : angle 4.74858 ( 2595) covalent geometry : bond 0.00481 (29505) covalent geometry : angle 0.78435 (39930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9729.59 seconds wall clock time: 173 minutes 33.59 seconds (10413.59 seconds total)