Starting phenix.real_space_refine on Tue May 27 04:42:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s91_40234/05_2025/8s91_40234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s91_40234/05_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_40234/05_2025/8s91_40234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s91_40234/05_2025/8s91_40234.map" model { file = "/net/cci-nas-00/data/ceres_data/8s91_40234/05_2025/8s91_40234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s91_40234/05_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 17.44, per 1000 atoms: 0.60 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: 7.53 Conformation dependent library (CDL) restraints added in 3.9 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: 3.71 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: 9.22 Time building geometry restraints manager: 8.74 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 63.280 Find NCS groups from input model: 1.300 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.870 ------------------------------------------------------------------------------- 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 : 3.233 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: 0.3798 time to fit residues: 365.9545 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 : 3.514 ------------------------------------------------------------------------------- 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 = 49882.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127708 restraints weight = 40625.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128577 restraints weight = 34770.648| |-----------------------------------------------------------------------------| 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 4.81653 ( 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 : 3.649 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: 0.6789 (mmm) cc_final: 0.6573 (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: 0.8188 (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: 0.5253 (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: 0.3654 time to fit residues: 353.6714 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 : 3.145 ------------------------------------------------------------------------------- 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: 0.6980 chunk 162 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 338 optimal weight: 0.0020 chunk 178 optimal weight: 3.9990 overall best weight: 1.6992 ------------------------------------------------------------------------------- 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 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** F 617 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.160611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121471 restraints weight = 49591.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122253 restraints weight = 38997.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123174 restraints weight = 32386.205| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29505 Z= 0.153 Angle : 0.672 8.130 39930 Z= 0.334 Chirality : 0.044 0.194 4626 Planarity : 0.005 0.066 5091 Dihedral : 8.893 165.607 4032 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.41 % Favored : 89.18 % Rotamer: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % 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: -1.64 (0.14), residues: 3603 helix: 0.61 (0.16), residues: 1284 sheet: -1.33 (0.23), residues: 525 loop : -2.38 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 519 HIS 0.010 0.001 HIS E 37 PHE 0.034 0.002 PHE E 13 TYR 0.020 0.002 TYR E 199 ARG 0.009 0.000 ARG A 445 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 907) hydrogen bonds : angle 4.54178 ( 2595) covalent geometry : bond 0.00351 (29505) covalent geometry : angle 0.67227 (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 618 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 615 time to evaluate : 3.291 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 128 LEU cc_start: 0.8876 (mt) cc_final: 0.8662 (mp) REVERT: A 315 LEU cc_start: 0.8625 (mt) cc_final: 0.8200 (mp) REVERT: A 387 LEU cc_start: 0.8903 (mt) cc_final: 0.8659 (pt) REVERT: A 391 TYR cc_start: 0.8653 (t80) cc_final: 0.8315 (t80) REVERT: A 538 SER cc_start: 0.8669 (m) cc_final: 0.8174 (p) REVERT: A 539 ILE cc_start: 0.8540 (tt) cc_final: 0.8266 (tt) REVERT: B 113 ASP cc_start: 0.7160 (t70) cc_final: 0.6924 (t70) REVERT: B 258 TYR cc_start: 0.8319 (t80) cc_final: 0.8056 (t80) REVERT: B 390 LEU cc_start: 0.9581 (mp) cc_final: 0.9340 (mp) REVERT: C 136 ASN cc_start: 0.9103 (m110) cc_final: 0.8821 (m-40) REVERT: C 151 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8277 (ttmm) REVERT: C 394 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8407 (tm-30) REVERT: D 51 ASN cc_start: 0.8703 (m-40) cc_final: 0.8430 (t0) REVERT: D 134 SER cc_start: 0.8430 (t) cc_final: 0.7875 (p) REVERT: D 287 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7692 (tm-30) REVERT: D 317 MET cc_start: 0.6636 (mmm) cc_final: 0.6154 (mmp) REVERT: D 521 MET cc_start: 0.8228 (ppp) cc_final: 0.8003 (ppp) REVERT: D 651 ARG cc_start: 0.8254 (tmm-80) cc_final: 0.7851 (tmm-80) REVERT: E 112 GLU cc_start: 0.8526 (mp0) cc_final: 0.7858 (tp30) REVERT: E 349 LEU cc_start: 0.7942 (tp) cc_final: 0.7669 (tp) REVERT: E 438 VAL cc_start: 0.7929 (m) cc_final: 0.7720 (p) REVERT: E 629 GLN cc_start: 0.8775 (tt0) cc_final: 0.7811 (tm-30) REVERT: E 651 ARG cc_start: 0.8078 (tmm-80) cc_final: 0.7792 (tmm-80) REVERT: F 51 ASN cc_start: 0.8596 (t0) cc_final: 0.8142 (t0) REVERT: F 146 MET cc_start: 0.5526 (pmm) cc_final: 0.4947 (ppp) REVERT: F 349 LEU cc_start: 0.8111 (tp) cc_final: 0.7699 (tp) REVERT: F 570 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7153 (tm-30) outliers start: 3 outliers final: 0 residues processed: 616 average time/residue: 0.3762 time to fit residues: 371.0976 Evaluate side-chains 418 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 3.205 ------------------------------------------------------------------------------- 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: 0.9990 chunk 76 optimal weight: 0.0870 chunk 345 optimal weight: 9.9990 chunk 211 optimal weight: 0.0060 chunk 274 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.3974 ------------------------------------------------------------------------------- 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 51 ASN D 434 GLN D 551 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.164459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125160 restraints weight = 48701.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126378 restraints weight = 37406.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127665 restraints weight = 30736.400| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29505 Z= 0.106 Angle : 0.629 8.326 39930 Z= 0.310 Chirality : 0.042 0.190 4626 Planarity : 0.004 0.066 5091 Dihedral : 8.644 174.372 4032 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.49 % Favored : 90.06 % Rotamer: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % 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: -1.51 (0.14), residues: 3603 helix: 0.71 (0.15), residues: 1302 sheet: -1.16 (0.23), residues: 519 loop : -2.35 (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 0.016 0.001 TYR B 391 ARG 0.005 0.000 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 907) hydrogen bonds : angle 4.22644 ( 2595) covalent geometry : bond 0.00227 (29505) covalent geometry : angle 0.62868 (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 606 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 605 time to evaluate : 3.453 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 128 LEU cc_start: 0.8901 (mt) cc_final: 0.8700 (mp) REVERT: A 352 MET cc_start: 0.7912 (tpp) cc_final: 0.7667 (tpp) REVERT: A 390 LEU cc_start: 0.9457 (mt) cc_final: 0.9157 (mt) REVERT: A 538 SER cc_start: 0.8665 (m) cc_final: 0.8127 (p) REVERT: A 539 ILE cc_start: 0.8429 (tt) cc_final: 0.8161 (tt) REVERT: B 113 ASP cc_start: 0.7146 (t70) cc_final: 0.6887 (t70) REVERT: B 258 TYR cc_start: 0.8256 (t80) cc_final: 0.7979 (t80) REVERT: B 289 GLN cc_start: 0.8190 (pp30) cc_final: 0.7500 (pp30) REVERT: B 352 MET cc_start: 0.7131 (mmm) cc_final: 0.6928 (tpp) REVERT: B 390 LEU cc_start: 0.9549 (mp) cc_final: 0.9111 (mp) REVERT: C 113 ASP cc_start: 0.6841 (t70) cc_final: 0.6585 (t70) REVERT: C 151 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8325 (ttmm) REVERT: D 134 SER cc_start: 0.8288 (t) cc_final: 0.7720 (p) REVERT: D 220 MET cc_start: 0.8151 (tpp) cc_final: 0.7905 (tpt) REVERT: D 287 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7786 (tm-30) REVERT: D 317 MET cc_start: 0.6540 (mmm) cc_final: 0.6119 (mmp) REVERT: D 349 LEU cc_start: 0.7687 (tp) cc_final: 0.7400 (tp) REVERT: D 521 MET cc_start: 0.8013 (ppp) cc_final: 0.7783 (ppp) REVERT: D 651 ARG cc_start: 0.8296 (tmm-80) cc_final: 0.7848 (tmm-80) REVERT: E 45 MET cc_start: 0.7000 (mmp) cc_final: 0.6791 (mmp) REVERT: E 112 GLU cc_start: 0.8532 (mp0) cc_final: 0.7888 (tp30) REVERT: E 166 PHE cc_start: 0.8513 (m-10) cc_final: 0.8199 (m-10) REVERT: E 289 GLU cc_start: 0.8929 (mp0) cc_final: 0.8260 (tp30) REVERT: E 349 LEU cc_start: 0.7770 (tp) cc_final: 0.7548 (tp) REVERT: E 438 VAL cc_start: 0.7918 (m) cc_final: 0.7649 (p) REVERT: E 651 ARG cc_start: 0.8157 (tmm-80) cc_final: 0.7828 (tmm-80) REVERT: F 32 ARG cc_start: 0.7596 (tpt90) cc_final: 0.7204 (tpt90) REVERT: F 51 ASN cc_start: 0.8534 (t0) cc_final: 0.8091 (t0) REVERT: F 146 MET cc_start: 0.5532 (pmm) cc_final: 0.5107 (ppp) REVERT: F 254 ASP cc_start: 0.9174 (m-30) cc_final: 0.8955 (m-30) REVERT: F 295 TYR cc_start: 0.8005 (m-80) cc_final: 0.7637 (m-80) REVERT: F 349 LEU cc_start: 0.8025 (tp) cc_final: 0.7668 (tp) REVERT: F 484 ASP cc_start: 0.7574 (m-30) cc_final: 0.7163 (m-30) REVERT: F 570 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7176 (tm-30) REVERT: F 651 ARG cc_start: 0.8274 (ttt180) cc_final: 0.7884 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 605 average time/residue: 0.3781 time to fit residues: 369.7266 Evaluate side-chains 434 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 3.377 ------------------------------------------------------------------------------- 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: 0.0980 chunk 21 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 339 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 179 optimal weight: 0.0770 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN E 448 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.162237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123118 restraints weight = 48476.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125000 restraints weight = 36668.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125833 restraints weight = 30042.976| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2322 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= 0.127 Angle : 0.649 8.905 39930 Z= 0.320 Chirality : 0.043 0.190 4626 Planarity : 0.004 0.065 5091 Dihedral : 8.510 173.737 4032 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.10 % Favored : 89.48 % Rotamer: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % 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: -1.54 (0.14), residues: 3603 helix: 0.69 (0.15), residues: 1305 sheet: -1.27 (0.22), residues: 567 loop : -2.36 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 519 HIS 0.005 0.001 HIS E 37 PHE 0.027 0.002 PHE D 13 TYR 0.019 0.001 TYR F 38 ARG 0.006 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 907) hydrogen bonds : angle 4.23328 ( 2595) covalent geometry : bond 0.00287 (29505) covalent geometry : angle 0.64937 (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 588 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 586 time to evaluate : 3.061 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 128 LEU cc_start: 0.8922 (mt) cc_final: 0.8706 (mp) REVERT: A 387 LEU cc_start: 0.8876 (mt) cc_final: 0.8635 (pt) REVERT: A 509 LEU cc_start: 0.8334 (mt) cc_final: 0.8095 (mt) REVERT: A 538 SER cc_start: 0.8799 (m) cc_final: 0.8226 (p) REVERT: B 113 ASP cc_start: 0.7100 (t70) cc_final: 0.6882 (t70) REVERT: B 258 TYR cc_start: 0.8266 (t80) cc_final: 0.8023 (t80) REVERT: B 289 GLN cc_start: 0.8387 (pp30) cc_final: 0.7672 (pp30) REVERT: B 418 GLU cc_start: 0.6982 (pm20) cc_final: 0.6102 (tp30) REVERT: C 113 ASP cc_start: 0.6798 (t70) cc_final: 0.6557 (t70) REVERT: C 151 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8355 (ttmm) REVERT: C 736 ASP cc_start: 0.7527 (m-30) cc_final: 0.6548 (m-30) REVERT: D 134 SER cc_start: 0.8472 (t) cc_final: 0.7911 (p) REVERT: D 287 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7853 (tm-30) REVERT: D 317 MET cc_start: 0.6703 (mmm) cc_final: 0.6294 (mmp) REVERT: D 349 LEU cc_start: 0.7804 (tp) cc_final: 0.7397 (tp) REVERT: D 519 TRP cc_start: 0.5060 (m-10) cc_final: 0.4735 (m-10) REVERT: D 521 MET cc_start: 0.8056 (ppp) cc_final: 0.7854 (ppp) REVERT: D 651 ARG cc_start: 0.8291 (tmm-80) cc_final: 0.7916 (tmm-80) REVERT: E 112 GLU cc_start: 0.8479 (mp0) cc_final: 0.7892 (tp30) REVERT: E 349 LEU cc_start: 0.8117 (tp) cc_final: 0.7815 (tp) REVERT: E 438 VAL cc_start: 0.7677 (m) cc_final: 0.7460 (p) REVERT: E 629 GLN cc_start: 0.8696 (tt0) cc_final: 0.7708 (tm-30) REVERT: E 651 ARG cc_start: 0.8134 (tmm-80) cc_final: 0.7738 (tmm-80) REVERT: F 1 MET cc_start: 0.3844 (mmt) cc_final: 0.3497 (mmp) REVERT: F 51 ASN cc_start: 0.8469 (t0) cc_final: 0.8027 (t0) REVERT: F 146 MET cc_start: 0.5579 (pmm) cc_final: 0.5010 (ppp) REVERT: F 166 PHE cc_start: 0.8560 (m-80) cc_final: 0.8231 (m-10) REVERT: F 254 ASP cc_start: 0.9175 (m-30) cc_final: 0.8961 (m-30) REVERT: F 349 LEU cc_start: 0.8311 (tp) cc_final: 0.7937 (tp) REVERT: F 493 LYS cc_start: 0.7888 (mppt) cc_final: 0.7600 (tmtt) REVERT: F 651 ARG cc_start: 0.8272 (ttt180) cc_final: 0.7812 (tmm-80) outliers start: 2 outliers final: 0 residues processed: 587 average time/residue: 0.3769 time to fit residues: 355.7877 Evaluate side-chains 422 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 3.267 ------------------------------------------------------------------------------- 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: 1.9990 chunk 253 optimal weight: 2.9990 chunk 350 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 364 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 305 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 A 536 GLN B 106 HIS ** 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 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** F 617 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.163317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129001 restraints weight = 46100.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129995 restraints weight = 38586.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130534 restraints weight = 31262.800| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29505 Z= 0.132 Angle : 0.662 9.071 39930 Z= 0.326 Chirality : 0.044 0.201 4626 Planarity : 0.004 0.065 5091 Dihedral : 8.439 172.468 4032 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.16 % Favored : 89.40 % Rotamer: Outliers : 0.09 % Allowed : 2.17 % Favored : 97.73 % 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: -1.55 (0.14), residues: 3603 helix: 0.78 (0.16), residues: 1275 sheet: -1.34 (0.21), residues: 597 loop : -2.38 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 292 HIS 0.007 0.001 HIS F 617 PHE 0.028 0.002 PHE D 13 TYR 0.018 0.001 TYR F 38 ARG 0.013 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 907) hydrogen bonds : angle 4.26299 ( 2595) covalent geometry : bond 0.00300 (29505) covalent geometry : angle 0.66246 (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 582 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 579 time to evaluate : 3.241 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 387 LEU cc_start: 0.8861 (mt) cc_final: 0.8641 (pt) REVERT: A 538 SER cc_start: 0.8699 (m) cc_final: 0.8213 (p) REVERT: A 539 ILE cc_start: 0.8432 (tt) cc_final: 0.8145 (tt) REVERT: B 289 GLN cc_start: 0.8288 (pp30) cc_final: 0.7579 (pp30) REVERT: B 391 TYR cc_start: 0.8030 (t80) cc_final: 0.7444 (t80) REVERT: C 101 LYS cc_start: 0.9219 (mttt) cc_final: 0.8699 (tppt) REVERT: C 151 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8414 (ttmm) REVERT: D 134 SER cc_start: 0.8626 (t) cc_final: 0.8118 (p) REVERT: D 201 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7923 (tt0) REVERT: D 287 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7929 (tm-30) REVERT: D 317 MET cc_start: 0.6623 (mmm) cc_final: 0.6269 (mmp) REVERT: D 349 LEU cc_start: 0.7844 (tp) cc_final: 0.7433 (tp) REVERT: D 521 MET cc_start: 0.8048 (ppp) cc_final: 0.7828 (ppp) REVERT: D 637 GLU cc_start: 0.7913 (tt0) cc_final: 0.7212 (tm-30) REVERT: D 651 ARG cc_start: 0.8293 (tmm-80) cc_final: 0.7910 (tmm-80) REVERT: E 112 GLU cc_start: 0.8397 (mp0) cc_final: 0.7849 (tp30) REVERT: E 166 PHE cc_start: 0.8392 (m-10) cc_final: 0.8166 (m-10) REVERT: E 349 LEU cc_start: 0.8028 (tp) cc_final: 0.7764 (tp) REVERT: E 438 VAL cc_start: 0.7740 (m) cc_final: 0.7528 (p) REVERT: E 629 GLN cc_start: 0.8605 (tt0) cc_final: 0.7554 (tm-30) REVERT: F 1 MET cc_start: 0.3967 (mmt) cc_final: 0.3616 (mmp) REVERT: F 51 ASN cc_start: 0.8567 (t0) cc_final: 0.8157 (t0) REVERT: F 146 MET cc_start: 0.5240 (pmm) cc_final: 0.4921 (ppp) REVERT: F 254 ASP cc_start: 0.9167 (m-30) cc_final: 0.8966 (m-30) REVERT: F 349 LEU cc_start: 0.8221 (tp) cc_final: 0.7858 (tp) REVERT: F 651 ARG cc_start: 0.8371 (ttt180) cc_final: 0.7837 (tmm-80) outliers start: 3 outliers final: 0 residues processed: 581 average time/residue: 0.3861 time to fit residues: 361.7405 Evaluate side-chains 402 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 3.172 ------------------------------------------------------------------------------- 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: 3.9990 chunk 294 optimal weight: 0.0870 chunk 265 optimal weight: 0.8980 chunk 274 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 314 optimal weight: 0.6980 chunk 364 optimal weight: 0.0370 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 C 480 ASN D 5 GLN D 434 GLN E 448 ASN E 560 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124738 restraints weight = 48239.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126500 restraints weight = 37477.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128452 restraints weight = 29411.006| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29505 Z= 0.106 Angle : 0.642 7.962 39930 Z= 0.315 Chirality : 0.043 0.181 4626 Planarity : 0.004 0.064 5091 Dihedral : 8.281 179.424 4032 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.24 % Favored : 90.34 % Rotamer: Outliers : 0.12 % Allowed : 1.18 % 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: -1.42 (0.14), residues: 3603 helix: 0.82 (0.15), residues: 1290 sheet: -1.08 (0.22), residues: 549 loop : -2.33 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 519 HIS 0.005 0.001 HIS E 37 PHE 0.023 0.001 PHE D 13 TYR 0.014 0.001 TYR C 201 ARG 0.007 0.000 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 907) hydrogen bonds : angle 4.08642 ( 2595) covalent geometry : bond 0.00228 (29505) covalent geometry : angle 0.64230 (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 582 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 578 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8509 (mt) cc_final: 0.8215 (mp) REVERT: A 538 SER cc_start: 0.8719 (m) cc_final: 0.8206 (p) REVERT: A 539 ILE cc_start: 0.8519 (tt) cc_final: 0.8241 (tt) REVERT: B 113 ASP cc_start: 0.6954 (t70) cc_final: 0.6741 (t70) REVERT: B 138 ILE cc_start: 0.8513 (tp) cc_final: 0.8299 (tp) REVERT: B 222 ARG cc_start: 0.6809 (tmm160) cc_final: 0.6572 (ttp80) REVERT: B 258 TYR cc_start: 0.8370 (t80) cc_final: 0.8136 (t80) REVERT: B 391 TYR cc_start: 0.8263 (t80) cc_final: 0.7907 (t80) REVERT: B 650 LEU cc_start: 0.6913 (mt) cc_final: 0.6687 (mp) REVERT: C 101 LYS cc_start: 0.9239 (mttt) cc_final: 0.8906 (mttp) REVERT: C 113 ASP cc_start: 0.6864 (t70) cc_final: 0.6649 (t70) REVERT: C 151 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8390 (tttp) REVERT: C 249 GLN cc_start: 0.8409 (pp30) cc_final: 0.8135 (pp30) REVERT: D 134 SER cc_start: 0.8529 (t) cc_final: 0.7981 (p) REVERT: D 201 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7879 (tt0) REVERT: D 287 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7939 (tm-30) REVERT: D 289 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8501 (mt-10) REVERT: D 311 CYS cc_start: 0.6017 (p) cc_final: 0.5815 (p) REVERT: D 317 MET cc_start: 0.6546 (mmm) cc_final: 0.6169 (mmp) REVERT: D 349 LEU cc_start: 0.7858 (tp) cc_final: 0.7456 (tp) REVERT: D 521 MET cc_start: 0.7968 (ppp) cc_final: 0.7754 (ppp) REVERT: D 637 GLU cc_start: 0.7921 (tt0) cc_final: 0.7077 (tm-30) REVERT: D 651 ARG cc_start: 0.8213 (tmm-80) cc_final: 0.7823 (tmm-80) REVERT: E 92 MET cc_start: 0.7390 (ttm) cc_final: 0.7103 (tpp) REVERT: E 112 GLU cc_start: 0.8408 (mp0) cc_final: 0.7857 (tp30) REVERT: E 289 GLU cc_start: 0.8716 (mp0) cc_final: 0.8177 (tp30) REVERT: E 349 LEU cc_start: 0.7988 (tp) cc_final: 0.7768 (tp) REVERT: E 438 VAL cc_start: 0.7785 (m) cc_final: 0.7526 (p) REVERT: E 629 GLN cc_start: 0.8659 (tt0) cc_final: 0.7594 (tm-30) REVERT: E 654 ARG cc_start: 0.7975 (ptp-170) cc_final: 0.7702 (ptp-170) REVERT: F 1 MET cc_start: 0.3504 (mmt) cc_final: 0.3162 (mmp) REVERT: F 51 ASN cc_start: 0.8436 (t0) cc_final: 0.8015 (t0) REVERT: F 146 MET cc_start: 0.5719 (pmm) cc_final: 0.5222 (ppp) REVERT: F 254 ASP cc_start: 0.9169 (m-30) cc_final: 0.8964 (m-30) REVERT: F 349 LEU cc_start: 0.8186 (tp) cc_final: 0.7855 (tp) REVERT: F 651 ARG cc_start: 0.8359 (ttt180) cc_final: 0.7793 (tmm-80) outliers start: 4 outliers final: 0 residues processed: 581 average time/residue: 0.3792 time to fit residues: 353.9420 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 : 3.175 ------------------------------------------------------------------------------- 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: 0.0010 chunk 299 optimal weight: 0.0270 chunk 294 optimal weight: 8.9990 chunk 183 optimal weight: 0.4980 chunk 171 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 339 optimal weight: 9.9990 chunk 324 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 overall best weight: 0.7048 ------------------------------------------------------------------------------- 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 D 434 GLN E 560 ASN ** F 5 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128936 restraints weight = 46474.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129424 restraints weight = 36221.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130259 restraints weight = 31217.274| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29505 Z= 0.111 Angle : 0.653 10.278 39930 Z= 0.319 Chirality : 0.043 0.184 4626 Planarity : 0.004 0.063 5091 Dihedral : 8.175 178.817 4032 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.99 % Favored : 89.59 % Rotamer: Outliers : 0.06 % Allowed : 1.06 % Favored : 98.88 % 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: -1.43 (0.14), residues: 3603 helix: 0.76 (0.15), residues: 1296 sheet: -1.01 (0.22), residues: 549 loop : -2.33 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 292 HIS 0.004 0.001 HIS E 37 PHE 0.023 0.001 PHE D 13 TYR 0.013 0.001 TYR A 391 ARG 0.008 0.000 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 907) hydrogen bonds : angle 4.13620 ( 2595) covalent geometry : bond 0.00244 (29505) covalent geometry : angle 0.65333 (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 568 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 566 time to evaluate : 3.416 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: 0.8521 (mt) cc_final: 0.8247 (mp) REVERT: A 390 LEU cc_start: 0.9465 (mt) cc_final: 0.9216 (mt) REVERT: A 538 SER cc_start: 0.8756 (m) cc_final: 0.8312 (p) REVERT: A 539 ILE cc_start: 0.8538 (tt) cc_final: 0.8253 (tt) REVERT: B 113 ASP cc_start: 0.6981 (t70) cc_final: 0.6773 (t70) REVERT: B 222 ARG cc_start: 0.6896 (tmm160) cc_final: 0.6656 (ttp80) REVERT: B 258 TYR cc_start: 0.8405 (t80) cc_final: 0.8168 (t80) REVERT: B 391 TYR cc_start: 0.8216 (t80) cc_final: 0.7775 (t80) REVERT: B 650 LEU cc_start: 0.7050 (mt) cc_final: 0.6675 (mp) REVERT: C 101 LYS cc_start: 0.9227 (mttt) cc_final: 0.8632 (tppt) REVERT: C 105 ARG cc_start: 0.8390 (mtm110) cc_final: 0.7939 (ptp90) REVERT: C 151 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8448 (ttmm) REVERT: C 249 GLN cc_start: 0.8408 (pp30) cc_final: 0.8141 (pp30) REVERT: D 31 GLU cc_start: 0.7972 (tp30) cc_final: 0.7570 (tp30) REVERT: D 134 SER cc_start: 0.8607 (t) cc_final: 0.8073 (p) REVERT: D 201 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7910 (tt0) REVERT: D 287 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 317 MET cc_start: 0.6679 (mmm) cc_final: 0.6411 (mmp) REVERT: D 349 LEU cc_start: 0.7785 (tp) cc_final: 0.7393 (tp) REVERT: D 519 TRP cc_start: 0.4656 (m-10) cc_final: 0.4377 (m-10) REVERT: D 521 MET cc_start: 0.8059 (ppp) cc_final: 0.7821 (ppp) REVERT: D 637 GLU cc_start: 0.8023 (tt0) cc_final: 0.7148 (tm-30) REVERT: D 651 ARG cc_start: 0.8273 (tmm-80) cc_final: 0.7865 (tmm-80) REVERT: E 92 MET cc_start: 0.7574 (ttm) cc_final: 0.7276 (tpp) REVERT: E 112 GLU cc_start: 0.8353 (mp0) cc_final: 0.7879 (tp30) REVERT: E 349 LEU cc_start: 0.8022 (tp) cc_final: 0.7784 (tp) REVERT: E 438 VAL cc_start: 0.7741 (m) cc_final: 0.7525 (p) REVERT: E 629 GLN cc_start: 0.8592 (tt0) cc_final: 0.7531 (tm-30) REVERT: E 654 ARG cc_start: 0.7968 (ptp-170) cc_final: 0.7767 (ptp-170) REVERT: F 1 MET cc_start: 0.3618 (mmt) cc_final: 0.3349 (mmp) REVERT: F 51 ASN cc_start: 0.8443 (t0) cc_final: 0.8029 (t0) REVERT: F 146 MET cc_start: 0.5373 (pmm) cc_final: 0.4976 (ppp) REVERT: F 254 ASP cc_start: 0.9192 (m-30) cc_final: 0.8985 (m-30) REVERT: F 295 TYR cc_start: 0.8386 (m-80) cc_final: 0.7078 (m-80) REVERT: F 349 LEU cc_start: 0.8200 (tp) cc_final: 0.7806 (tp) outliers start: 2 outliers final: 0 residues processed: 567 average time/residue: 0.3694 time to fit residues: 338.1916 Evaluate side-chains 408 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 3.599 ------------------------------------------------------------------------------- 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: 10.0000 chunk 183 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 295 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 179 optimal weight: 0.0050 chunk 71 optimal weight: 0.7980 chunk 270 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS B 289 GLN C 171 HIS D 434 GLN E 448 ASN E 560 ASN ** F 5 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.163001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124188 restraints weight = 47664.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126289 restraints weight = 36379.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128048 restraints weight = 28655.581| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29505 Z= 0.111 Angle : 0.658 10.518 39930 Z= 0.322 Chirality : 0.043 0.204 4626 Planarity : 0.004 0.062 5091 Dihedral : 8.064 176.731 4032 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.44 % Favored : 90.12 % Rotamer: Outliers : 0.12 % Allowed : 0.71 % Favored : 99.16 % 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: -1.39 (0.14), residues: 3603 helix: 0.79 (0.16), residues: 1287 sheet: -0.90 (0.23), residues: 537 loop : -2.32 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 519 HIS 0.005 0.001 HIS C 449 PHE 0.027 0.001 PHE D 61 TYR 0.020 0.001 TYR C 752 ARG 0.007 0.000 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 907) hydrogen bonds : angle 4.15831 ( 2595) covalent geometry : bond 0.00243 (29505) covalent geometry : angle 0.65797 (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 561 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 557 time to evaluate : 3.526 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 315 LEU cc_start: 0.8507 (mt) cc_final: 0.8203 (mp) REVERT: A 394 GLN cc_start: 0.8657 (mp10) cc_final: 0.8213 (mp10) REVERT: A 538 SER cc_start: 0.8859 (m) cc_final: 0.8392 (p) REVERT: A 539 ILE cc_start: 0.8516 (tt) cc_final: 0.8229 (tt) REVERT: B 113 ASP cc_start: 0.6993 (t70) cc_final: 0.6784 (t70) REVERT: B 222 ARG cc_start: 0.6772 (tmm160) cc_final: 0.6555 (ttp80) REVERT: B 258 TYR cc_start: 0.8412 (t80) cc_final: 0.8169 (t80) REVERT: B 289 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7554 (pp30) REVERT: B 391 TYR cc_start: 0.8361 (t80) cc_final: 0.7832 (t80) REVERT: C 101 LYS cc_start: 0.9210 (mttt) cc_final: 0.8673 (tppt) REVERT: C 151 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8369 (ttmm) REVERT: C 249 GLN cc_start: 0.8413 (pp30) cc_final: 0.8149 (pp30) REVERT: C 331 ILE cc_start: 0.8612 (mt) cc_final: 0.8380 (pt) REVERT: D 31 GLU cc_start: 0.7949 (tp30) cc_final: 0.7535 (tp30) REVERT: D 134 SER cc_start: 0.8594 (t) cc_final: 0.8002 (p) REVERT: D 201 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7910 (tt0) REVERT: D 220 MET cc_start: 0.8057 (tpp) cc_final: 0.7673 (tpt) REVERT: D 245 MET cc_start: 0.7637 (mmm) cc_final: 0.7258 (mmm) REVERT: D 287 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8014 (tm-30) REVERT: D 317 MET cc_start: 0.6598 (mmm) cc_final: 0.6282 (mmp) REVERT: D 349 LEU cc_start: 0.7786 (tp) cc_final: 0.7409 (tp) REVERT: D 496 ASP cc_start: 0.7920 (t0) cc_final: 0.7659 (t0) REVERT: D 519 TRP cc_start: 0.4859 (m-10) cc_final: 0.4611 (m-10) REVERT: D 521 MET cc_start: 0.8153 (ppp) cc_final: 0.7835 (ppp) REVERT: D 552 MET cc_start: 0.8265 (tpp) cc_final: 0.8057 (tpt) REVERT: D 637 GLU cc_start: 0.7894 (tt0) cc_final: 0.7056 (tm-30) REVERT: E 45 MET cc_start: 0.7111 (mmp) cc_final: 0.6828 (mmp) REVERT: E 92 MET cc_start: 0.7525 (ttm) cc_final: 0.7219 (tpp) REVERT: E 112 GLU cc_start: 0.8403 (mp0) cc_final: 0.7626 (tp30) REVERT: E 114 ILE cc_start: 0.8265 (mm) cc_final: 0.8010 (tp) REVERT: E 166 PHE cc_start: 0.8411 (m-10) cc_final: 0.8183 (m-10) REVERT: E 349 LEU cc_start: 0.8059 (tp) cc_final: 0.7829 (tp) REVERT: E 438 VAL cc_start: 0.7807 (m) cc_final: 0.7567 (p) REVERT: E 629 GLN cc_start: 0.8632 (tt0) cc_final: 0.7671 (tm-30) REVERT: E 654 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7709 (ptp-170) REVERT: F 1 MET cc_start: 0.3445 (mmt) cc_final: 0.3093 (mmp) REVERT: F 51 ASN cc_start: 0.8305 (t0) cc_final: 0.7934 (t0) REVERT: F 60 MET cc_start: 0.7673 (tmm) cc_final: 0.6394 (tmm) REVERT: F 146 MET cc_start: 0.5510 (pmm) cc_final: 0.5030 (ppp) REVERT: F 254 ASP cc_start: 0.9160 (m-30) cc_final: 0.8940 (m-30) REVERT: F 349 LEU cc_start: 0.8284 (tp) cc_final: 0.7903 (tp) REVERT: F 651 ARG cc_start: 0.8274 (ttt180) cc_final: 0.7861 (tmm-80) outliers start: 4 outliers final: 0 residues processed: 559 average time/residue: 0.3696 time to fit residues: 333.2592 Evaluate side-chains 407 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 406 time to evaluate : 3.200 ------------------------------------------------------------------------------- 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: 7.9990 chunk 152 optimal weight: 3.9990 chunk 242 optimal weight: 0.0770 chunk 126 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 271 optimal weight: 0.6980 chunk 359 optimal weight: 5.9990 chunk 364 optimal weight: 4.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN E 59 ASN E 560 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120223 restraints weight = 48993.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121292 restraints weight = 37828.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122124 restraints weight = 30956.842| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29505 Z= 0.158 Angle : 0.713 11.113 39930 Z= 0.351 Chirality : 0.045 0.197 4626 Planarity : 0.005 0.065 5091 Dihedral : 8.163 175.084 4032 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.19 % Favored : 88.40 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.53 % 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: -1.54 (0.14), residues: 3603 helix: 0.73 (0.15), residues: 1275 sheet: -1.18 (0.21), residues: 597 loop : -2.40 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 292 HIS 0.008 0.001 HIS D 617 PHE 0.025 0.002 PHE E 13 TYR 0.023 0.001 TYR E 199 ARG 0.009 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 907) hydrogen bonds : angle 4.35222 ( 2595) covalent geometry : bond 0.00364 (29505) covalent geometry : angle 0.71313 (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 544 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 541 time to evaluate : 3.282 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 155 CYS cc_start: 0.8943 (m) cc_final: 0.8742 (m) REVERT: A 538 SER cc_start: 0.8901 (m) cc_final: 0.8443 (p) REVERT: A 539 ILE cc_start: 0.8536 (tt) cc_final: 0.8269 (tt) REVERT: B 113 ASP cc_start: 0.7071 (t70) cc_final: 0.6539 (t70) REVERT: B 258 TYR cc_start: 0.8559 (t80) cc_final: 0.8322 (t80) REVERT: B 731 GLU cc_start: 0.7356 (tp30) cc_final: 0.7155 (tp30) REVERT: C 101 LYS cc_start: 0.9209 (mttt) cc_final: 0.8705 (tppt) REVERT: C 151 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8440 (ttmm) REVERT: C 249 GLN cc_start: 0.8404 (pp30) cc_final: 0.8022 (pp30) REVERT: D 31 GLU cc_start: 0.8016 (tp30) cc_final: 0.7608 (tp30) REVERT: D 134 SER cc_start: 0.8863 (t) cc_final: 0.8319 (p) REVERT: D 146 MET cc_start: 0.7246 (pmm) cc_final: 0.6802 (ppp) REVERT: D 201 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8040 (tt0) REVERT: D 287 GLU cc_start: 0.8625 (tm-30) cc_final: 0.7929 (tm-30) REVERT: D 317 MET cc_start: 0.6726 (mmm) cc_final: 0.6408 (mmp) REVERT: D 519 TRP cc_start: 0.5176 (m-10) cc_final: 0.4960 (m-10) REVERT: D 637 GLU cc_start: 0.7860 (tt0) cc_final: 0.7039 (tm-30) REVERT: D 651 ARG cc_start: 0.8242 (tmm-80) cc_final: 0.7810 (tmm-80) REVERT: E 45 MET cc_start: 0.7066 (mmp) cc_final: 0.6317 (mmp) REVERT: E 92 MET cc_start: 0.7684 (ttm) cc_final: 0.7327 (tpp) REVERT: E 112 GLU cc_start: 0.8500 (mp0) cc_final: 0.7859 (tp30) REVERT: E 438 VAL cc_start: 0.7940 (m) cc_final: 0.7689 (p) REVERT: E 629 GLN cc_start: 0.8708 (tt0) cc_final: 0.7705 (tm-30) REVERT: E 654 ARG cc_start: 0.8007 (ptp-170) cc_final: 0.7737 (ptp-170) REVERT: F 1 MET cc_start: 0.3624 (mmt) cc_final: 0.3237 (mmp) REVERT: F 51 ASN cc_start: 0.8313 (t0) cc_final: 0.7835 (t0) REVERT: F 60 MET cc_start: 0.7634 (tmm) cc_final: 0.6911 (tmm) REVERT: F 146 MET cc_start: 0.5674 (pmm) cc_final: 0.5085 (ppp) REVERT: F 254 ASP cc_start: 0.9220 (m-30) cc_final: 0.9012 (m-30) REVERT: F 295 TYR cc_start: 0.8483 (m-80) cc_final: 0.7130 (m-80) REVERT: F 349 LEU cc_start: 0.8371 (tp) cc_final: 0.8024 (tp) outliers start: 3 outliers final: 0 residues processed: 543 average time/residue: 0.3732 time to fit residues: 327.3939 Evaluate side-chains 399 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 3.155 ------------------------------------------------------------------------------- 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: 1.9990 chunk 343 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN E 59 ASN E 448 ASN E 560 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.158285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120117 restraints weight = 48817.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121025 restraints weight = 38023.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121895 restraints weight = 31287.942| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29505 Z= 0.155 Angle : 0.721 10.359 39930 Z= 0.356 Chirality : 0.045 0.255 4626 Planarity : 0.005 0.062 5091 Dihedral : 8.218 172.818 4032 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.74 % Favored : 88.84 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % 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: -1.62 (0.14), residues: 3603 helix: 0.65 (0.15), residues: 1275 sheet: -1.19 (0.21), residues: 594 loop : -2.44 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 519 HIS 0.006 0.001 HIS C 449 PHE 0.033 0.002 PHE D 61 TYR 0.024 0.001 TYR B 391 ARG 0.008 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 907) hydrogen bonds : angle 4.42792 ( 2595) covalent geometry : bond 0.00357 (29505) covalent geometry : angle 0.72080 (39930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8796.00 seconds wall clock time: 155 minutes 7.40 seconds (9307.40 seconds total)