Starting phenix.real_space_refine on Mon Aug 25 15:36:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s91_40234/08_2025/8s91_40234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s91_40234/08_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_40234/08_2025/8s91_40234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s91_40234/08_2025/8s91_40234.map" model { file = "/net/cci-nas-00/data/ceres_data/8s91_40234/08_2025/8s91_40234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s91_40234/08_2025/8s91_40234.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.24, per 1000 atoms: 0.25 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: 2.17 Conformation dependent library (CDL) restraints added in 946.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.01 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: 4.25 Time building geometry restraints manager: 2.80 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.350 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG D 559 TYR 0.023 0.001 TYR B 391 PHE 0.022 0.001 PHE B 102 TRP 0.015 0.001 TRP E 292 HIS 0.010 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00255 (29505) covalent geometry : angle 0.71129 (39930) hydrogen bonds : bond 0.20258 ( 907) hydrogen bonds : angle 6.67544 ( 2595) *********************** 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 : 0.969 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 329 VAL cc_start: 0.9124 (m) cc_final: 0.8773 (p) REVERT: A 391 TYR cc_start: 0.8559 (t80) cc_final: 0.8315 (t80) REVERT: B 113 ASP cc_start: 0.6985 (t70) cc_final: 0.6726 (t70) REVERT: B 258 TYR cc_start: 0.7986 (t80) cc_final: 0.7682 (t80) REVERT: C 136 ASN cc_start: 0.8992 (m-40) cc_final: 0.8775 (m-40) REVERT: C 151 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8077 (ttmm) REVERT: D 20 TYR cc_start: 0.6900 (m-10) cc_final: 0.6081 (m-10) REVERT: D 52 MET cc_start: 0.7995 (pmm) cc_final: 0.7634 (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: 0.6937 (mmt) REVERT: D 641 LEU cc_start: 0.8710 (mt) cc_final: 0.8509 (mp) REVERT: E 47 LEU cc_start: 0.8029 (tp) cc_final: 0.7823 (tp) REVERT: E 114 ILE cc_start: 0.8025 (mm) cc_final: 0.7542 (tp) REVERT: F 51 ASN cc_start: 0.8957 (t0) cc_final: 0.8519 (t0) REVERT: F 60 MET cc_start: 0.8116 (ttt) cc_final: 0.7648 (ttt) REVERT: F 146 MET cc_start: 0.5218 (pmm) cc_final: 0.4709 (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: 0.1546 time to fit residues: 149.8361 Evaluate side-chains 427 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN 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 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 HIS C 608 HIS D 59 ASN D 152 HIS D 162 GLN D 209 GLN D 433 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 433 GLN E 448 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123195 restraints weight = 51017.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123204 restraints weight = 42277.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124176 restraints weight = 38480.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124782 restraints weight = 34340.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125105 restraints weight = 30318.906| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29505 Z= 0.190 Angle : 0.702 9.180 39930 Z= 0.352 Chirality : 0.045 0.191 4626 Planarity : 0.005 0.069 5091 Dihedral : 9.222 159.995 4032 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.71 % Favored : 88.84 % Rotamer: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.14), residues: 3603 helix: 0.53 (0.15), residues: 1284 sheet: -1.47 (0.22), residues: 579 loop : -2.47 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 99 TYR 0.026 0.002 TYR E 199 PHE 0.023 0.002 PHE D 13 TRP 0.017 0.002 TRP D 292 HIS 0.008 0.002 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00428 (29505) covalent geometry : angle 0.70203 (39930) hydrogen bonds : bond 0.04168 ( 907) hydrogen bonds : angle 4.87215 ( 2595) *********************** 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 589 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 585 time to evaluate : 0.815 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 238 MET cc_start: 0.8970 (ppp) cc_final: 0.8342 (ppp) REVERT: A 315 LEU cc_start: 0.8649 (mt) cc_final: 0.8224 (mp) REVERT: A 387 LEU cc_start: 0.8886 (mt) cc_final: 0.8634 (pt) REVERT: A 391 TYR cc_start: 0.8510 (t80) cc_final: 0.8163 (t80) REVERT: A 523 MET cc_start: 0.5014 (mtt) cc_final: 0.4761 (mtt) REVERT: A 538 SER cc_start: 0.8526 (m) cc_final: 0.8118 (p) REVERT: A 539 ILE cc_start: 0.8516 (tt) cc_final: 0.8203 (tt) REVERT: A 657 THR cc_start: 0.7734 (m) cc_final: 0.7509 (t) REVERT: B 113 ASP cc_start: 0.7156 (t70) cc_final: 0.6935 (t70) REVERT: B 258 TYR cc_start: 0.8313 (t80) cc_final: 0.8084 (t80) REVERT: B 390 LEU cc_start: 0.9554 (mp) cc_final: 0.9276 (mp) REVERT: B 391 TYR cc_start: 0.8351 (t80) cc_final: 0.8057 (t80) REVERT: C 113 ASP cc_start: 0.7171 (t70) cc_final: 0.6615 (t70) REVERT: C 151 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8265 (ttmm) REVERT: C 736 ASP cc_start: 0.7819 (m-30) cc_final: 0.7608 (m-30) REVERT: D 52 MET cc_start: 0.7961 (pmm) cc_final: 0.7458 (tmm) REVERT: D 134 SER cc_start: 0.8282 (t) cc_final: 0.7880 (p) REVERT: D 201 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7912 (tt0) REVERT: D 287 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7681 (tm-30) REVERT: D 317 MET cc_start: 0.6839 (mmm) cc_final: 0.6347 (mmp) REVERT: D 453 ILE cc_start: 0.8709 (mm) cc_final: 0.8488 (mm) REVERT: D 594 ILE cc_start: 0.8229 (tp) cc_final: 0.7946 (tp) REVERT: D 641 LEU cc_start: 0.8920 (mt) cc_final: 0.8690 (mp) REVERT: E 295 TYR cc_start: 0.8301 (m-80) cc_final: 0.7815 (m-80) REVERT: E 522 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8030 (mm-30) REVERT: E 595 THR cc_start: 0.7621 (m) cc_final: 0.7175 (p) REVERT: E 651 ARG cc_start: 0.8120 (tmm-80) cc_final: 0.7844 (tmm-80) REVERT: F 51 ASN cc_start: 0.8755 (t0) cc_final: 0.8180 (t0) REVERT: F 146 MET cc_start: 0.5383 (pmm) cc_final: 0.4898 (ppp) outliers start: 4 outliers final: 0 residues processed: 588 average time/residue: 0.1565 time to fit residues: 150.2916 Evaluate side-chains 417 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 345 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 394 GLN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN D 5 GLN D 59 ASN D 434 GLN E 59 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.159582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121680 restraints weight = 49585.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122286 restraints weight = 37059.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122745 restraints weight = 32047.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123390 restraints weight = 30399.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123906 restraints weight = 27686.264| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29505 Z= 0.160 Angle : 0.676 8.192 39930 Z= 0.338 Chirality : 0.044 0.197 4626 Planarity : 0.005 0.067 5091 Dihedral : 8.917 162.794 4032 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.94 % Favored : 89.65 % Rotamer: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.14), residues: 3603 helix: 0.51 (0.15), residues: 1281 sheet: -1.52 (0.22), residues: 564 loop : -2.44 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 718 TYR 0.019 0.002 TYR C 75 PHE 0.037 0.002 PHE E 13 TRP 0.007 0.002 TRP F 248 HIS 0.009 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00368 (29505) covalent geometry : angle 0.67573 (39930) hydrogen bonds : bond 0.04109 ( 907) hydrogen bonds : angle 4.62485 ( 2595) *********************** 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 599 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 596 time to evaluate : 1.074 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 315 LEU cc_start: 0.8692 (mt) cc_final: 0.8299 (mp) REVERT: A 391 TYR cc_start: 0.8637 (t80) cc_final: 0.8176 (t80) REVERT: A 538 SER cc_start: 0.8669 (m) cc_final: 0.8192 (p) REVERT: A 539 ILE cc_start: 0.8542 (tt) cc_final: 0.8276 (tt) REVERT: B 113 ASP cc_start: 0.7122 (t70) cc_final: 0.6886 (t70) REVERT: B 258 TYR cc_start: 0.8367 (t80) cc_final: 0.8137 (t80) REVERT: B 289 GLN cc_start: 0.8336 (pp30) cc_final: 0.7681 (pp30) REVERT: B 390 LEU cc_start: 0.9537 (mp) cc_final: 0.9313 (mp) REVERT: C 136 ASN cc_start: 0.9082 (m110) cc_final: 0.8798 (m-40) REVERT: C 151 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8275 (ttmm) REVERT: D 52 MET cc_start: 0.8064 (pmm) cc_final: 0.7817 (tmm) REVERT: D 134 SER cc_start: 0.8510 (t) cc_final: 0.8060 (p) REVERT: D 201 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7934 (tt0) REVERT: D 287 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7691 (tm-30) REVERT: D 317 MET cc_start: 0.6743 (mmm) cc_final: 0.6254 (mmp) REVERT: D 451 THR cc_start: 0.8990 (p) cc_final: 0.8625 (m) REVERT: D 521 MET cc_start: 0.8240 (ppp) cc_final: 0.8034 (ppp) REVERT: D 641 LEU cc_start: 0.8866 (mt) cc_final: 0.8617 (mp) REVERT: E 92 MET cc_start: 0.6969 (ttm) cc_final: 0.6768 (tpp) REVERT: E 112 GLU cc_start: 0.8554 (mp0) cc_final: 0.7916 (tp30) REVERT: E 295 TYR cc_start: 0.8603 (m-80) cc_final: 0.8165 (m-80) REVERT: E 349 LEU cc_start: 0.7920 (tp) cc_final: 0.7613 (tp) REVERT: E 629 GLN cc_start: 0.8695 (tt0) cc_final: 0.7678 (tm-30) REVERT: E 651 ARG cc_start: 0.8128 (tmm-80) cc_final: 0.7829 (tmm-80) REVERT: F 51 ASN cc_start: 0.8653 (t0) cc_final: 0.8215 (t0) REVERT: F 146 MET cc_start: 0.5513 (pmm) cc_final: 0.4946 (ppp) REVERT: F 295 TYR cc_start: 0.8063 (m-80) cc_final: 0.7050 (m-80) REVERT: F 317 MET cc_start: 0.6729 (mtm) cc_final: 0.6512 (mtp) REVERT: F 349 LEU cc_start: 0.8240 (tp) cc_final: 0.7797 (tp) REVERT: F 493 LYS cc_start: 0.7925 (mppt) cc_final: 0.7624 (tmtt) REVERT: F 570 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7192 (tm-30) outliers start: 3 outliers final: 0 residues processed: 598 average time/residue: 0.1624 time to fit residues: 156.0412 Evaluate side-chains 417 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 216 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 310 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 294 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 394 GLN C 171 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 434 GLN E 59 ASN E 448 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 627 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN F 617 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120677 restraints weight = 48761.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120930 restraints weight = 36900.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121428 restraints weight = 33624.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122237 restraints weight = 30503.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123250 restraints weight = 27455.708| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29505 Z= 0.155 Angle : 0.678 9.447 39930 Z= 0.336 Chirality : 0.044 0.188 4626 Planarity : 0.005 0.066 5091 Dihedral : 8.744 163.172 4032 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.69 % Favored : 88.87 % Rotamer: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.14), residues: 3603 helix: 0.57 (0.15), residues: 1284 sheet: -1.56 (0.21), residues: 567 loop : -2.48 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 649 TYR 0.021 0.001 TYR E 199 PHE 0.032 0.002 PHE E 13 TRP 0.011 0.002 TRP E 292 HIS 0.007 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00356 (29505) covalent geometry : angle 0.67763 (39930) hydrogen bonds : bond 0.03840 ( 907) hydrogen bonds : angle 4.48368 ( 2595) *********************** 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 574 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 572 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8710 (mt) cc_final: 0.8321 (mp) REVERT: A 391 TYR cc_start: 0.8743 (t80) cc_final: 0.8456 (t80) REVERT: A 538 SER cc_start: 0.8731 (m) cc_final: 0.8212 (p) REVERT: A 539 ILE cc_start: 0.8624 (tt) cc_final: 0.8366 (tt) REVERT: B 113 ASP cc_start: 0.7191 (t70) cc_final: 0.6957 (t70) REVERT: B 258 TYR cc_start: 0.8442 (t80) cc_final: 0.8162 (t80) REVERT: B 390 LEU cc_start: 0.9518 (mp) cc_final: 0.9076 (mp) REVERT: B 731 GLU cc_start: 0.7372 (tp30) cc_final: 0.7138 (tp30) REVERT: C 136 ASN cc_start: 0.9126 (m110) cc_final: 0.8850 (m-40) REVERT: C 151 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8405 (ttmm) REVERT: D 45 MET cc_start: 0.7640 (mmp) cc_final: 0.7405 (tpp) REVERT: D 51 ASN cc_start: 0.8409 (t0) cc_final: 0.8053 (t0) REVERT: D 52 MET cc_start: 0.8443 (pmm) cc_final: 0.7996 (tmm) REVERT: D 99 ARG cc_start: 0.6915 (mpt90) cc_final: 0.6634 (mmt180) REVERT: D 134 SER cc_start: 0.8635 (t) cc_final: 0.8159 (p) REVERT: D 201 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7970 (tt0) REVERT: D 220 MET cc_start: 0.8386 (tpp) cc_final: 0.8159 (tpt) REVERT: D 287 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7853 (tm-30) REVERT: D 317 MET cc_start: 0.6678 (mmm) cc_final: 0.6343 (mmp) REVERT: D 519 TRP cc_start: 0.5353 (m-10) cc_final: 0.5145 (m-10) REVERT: D 521 MET cc_start: 0.8176 (ppp) cc_final: 0.7967 (ppp) REVERT: D 641 LEU cc_start: 0.8973 (mt) cc_final: 0.8702 (mp) REVERT: E 92 MET cc_start: 0.7196 (ttm) cc_final: 0.6888 (tpp) REVERT: E 112 GLU cc_start: 0.8510 (mp0) cc_final: 0.7896 (tp30) REVERT: E 295 TYR cc_start: 0.8631 (m-80) cc_final: 0.8049 (m-80) REVERT: E 349 LEU cc_start: 0.8109 (tp) cc_final: 0.7802 (tp) REVERT: E 595 THR cc_start: 0.7500 (m) cc_final: 0.7013 (p) REVERT: E 629 GLN cc_start: 0.8672 (tt0) cc_final: 0.7633 (tm-30) REVERT: F 51 ASN cc_start: 0.8622 (t0) cc_final: 0.8149 (t0) REVERT: F 146 MET cc_start: 0.5644 (pmm) cc_final: 0.5033 (ppp) REVERT: F 166 PHE cc_start: 0.8410 (m-80) cc_final: 0.8180 (m-80) REVERT: F 254 ASP cc_start: 0.9263 (m-30) cc_final: 0.9000 (m-30) REVERT: F 295 TYR cc_start: 0.8246 (m-80) cc_final: 0.7277 (m-80) REVERT: F 317 MET cc_start: 0.6697 (mtm) cc_final: 0.6426 (mtp) REVERT: F 349 LEU cc_start: 0.8214 (tp) cc_final: 0.7727 (tp) outliers start: 2 outliers final: 0 residues processed: 574 average time/residue: 0.1641 time to fit residues: 152.0649 Evaluate side-chains 391 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 199 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 0.0370 chunk 363 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 354 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- 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 600 HIS C 171 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 2 ASN D 59 ASN D 434 GLN ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117889 restraints weight = 49557.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117975 restraints weight = 38457.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118106 restraints weight = 35228.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118909 restraints weight = 32567.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119541 restraints weight = 29569.560| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29505 Z= 0.192 Angle : 0.725 11.822 39930 Z= 0.361 Chirality : 0.045 0.189 4626 Planarity : 0.005 0.065 5091 Dihedral : 8.769 157.589 4032 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.60 % Favored : 87.98 % Rotamer: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.14), residues: 3603 helix: 0.41 (0.15), residues: 1293 sheet: -1.66 (0.21), residues: 576 loop : -2.50 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 718 TYR 0.020 0.002 TYR E 199 PHE 0.032 0.002 PHE E 13 TRP 0.011 0.002 TRP D 519 HIS 0.009 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00447 (29505) covalent geometry : angle 0.72488 (39930) hydrogen bonds : bond 0.04241 ( 907) hydrogen bonds : angle 4.62851 ( 2595) *********************** 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 567 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 564 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9031 (mt) cc_final: 0.8771 (pt) REVERT: A 390 LEU cc_start: 0.9508 (mt) cc_final: 0.9206 (mt) REVERT: A 538 SER cc_start: 0.8949 (m) cc_final: 0.8429 (p) REVERT: A 539 ILE cc_start: 0.8664 (tt) cc_final: 0.8434 (tt) REVERT: A 576 ASN cc_start: 0.8438 (m110) cc_final: 0.7913 (t0) REVERT: A 658 ILE cc_start: 0.7843 (pt) cc_final: 0.7571 (pt) REVERT: B 113 ASP cc_start: 0.7080 (t70) cc_final: 0.6855 (t70) REVERT: B 289 GLN cc_start: 0.8430 (pp30) cc_final: 0.7658 (pp30) REVERT: B 390 LEU cc_start: 0.9525 (mp) cc_final: 0.9232 (mp) REVERT: B 418 GLU cc_start: 0.7005 (pm20) cc_final: 0.6228 (tp30) REVERT: C 136 ASN cc_start: 0.9102 (m110) cc_final: 0.8836 (m-40) REVERT: C 151 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8405 (ttmm) REVERT: D 45 MET cc_start: 0.7926 (mmp) cc_final: 0.7572 (tpp) REVERT: D 51 ASN cc_start: 0.8532 (t0) cc_final: 0.8228 (t0) REVERT: D 52 MET cc_start: 0.8481 (pmm) cc_final: 0.8051 (tmm) REVERT: D 134 SER cc_start: 0.8809 (t) cc_final: 0.8334 (p) REVERT: D 201 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8041 (tt0) REVERT: D 287 GLU cc_start: 0.8521 (tm-30) cc_final: 0.7982 (tm-30) REVERT: D 317 MET cc_start: 0.6624 (mmm) cc_final: 0.6269 (mmp) REVERT: D 521 MET cc_start: 0.8156 (ppp) cc_final: 0.7940 (ppp) REVERT: D 637 GLU cc_start: 0.7981 (tt0) cc_final: 0.7257 (tm-30) REVERT: D 641 LEU cc_start: 0.8979 (mt) cc_final: 0.8694 (mp) REVERT: E 112 GLU cc_start: 0.8518 (mp0) cc_final: 0.7800 (tp30) REVERT: E 146 MET cc_start: 0.6693 (ppp) cc_final: 0.6257 (ppp) REVERT: E 349 LEU cc_start: 0.8208 (tp) cc_final: 0.7949 (tp) REVERT: E 595 THR cc_start: 0.7520 (m) cc_final: 0.7191 (p) REVERT: E 629 GLN cc_start: 0.8735 (tt0) cc_final: 0.7634 (tm-30) REVERT: F 51 ASN cc_start: 0.8632 (t0) cc_final: 0.8186 (t0) REVERT: F 146 MET cc_start: 0.6056 (pmm) cc_final: 0.5356 (ppp) REVERT: F 254 ASP cc_start: 0.9238 (m-30) cc_final: 0.8989 (m-30) REVERT: F 295 TYR cc_start: 0.8305 (m-80) cc_final: 0.7197 (m-80) REVERT: F 317 MET cc_start: 0.6603 (mtm) cc_final: 0.6382 (mtp) REVERT: F 349 LEU cc_start: 0.8231 (tp) cc_final: 0.7816 (tp) outliers start: 3 outliers final: 0 residues processed: 567 average time/residue: 0.1849 time to fit residues: 169.7643 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 : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 141 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 185 optimal weight: 0.4980 chunk 200 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 197 optimal weight: 0.0870 chunk 351 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 536 GLN B 106 HIS B 171 HIS B 600 HIS C 171 HIS C 213 ASN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 GLN D 59 ASN E 59 ASN E 448 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123855 restraints weight = 50560.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123518 restraints weight = 46498.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124918 restraints weight = 42386.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.125379 restraints weight = 36191.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125648 restraints weight = 32815.464| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29505 Z= 0.114 Angle : 0.655 8.349 39930 Z= 0.325 Chirality : 0.043 0.180 4626 Planarity : 0.004 0.065 5091 Dihedral : 8.509 164.415 4032 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.13 % Favored : 89.43 % Rotamer: Outliers : 0.12 % Allowed : 2.36 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.14), residues: 3603 helix: 0.66 (0.15), residues: 1266 sheet: -1.55 (0.21), residues: 603 loop : -2.46 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 32 TYR 0.018 0.001 TYR B 391 PHE 0.024 0.001 PHE D 13 TRP 0.010 0.002 TRP E 248 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00252 (29505) covalent geometry : angle 0.65475 (39930) hydrogen bonds : bond 0.03407 ( 907) hydrogen bonds : angle 4.30459 ( 2595) *********************** 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 570 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 566 time to evaluate : 1.278 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 387 LEU cc_start: 0.8845 (mt) cc_final: 0.8623 (pt) REVERT: A 400 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6959 (mt-10) REVERT: A 538 SER cc_start: 0.8805 (m) cc_final: 0.8223 (p) REVERT: B 113 ASP cc_start: 0.6879 (t70) cc_final: 0.6645 (t70) REVERT: B 237 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8072 (tppt) REVERT: B 289 GLN cc_start: 0.8433 (pp30) cc_final: 0.7679 (pp30) REVERT: B 390 LEU cc_start: 0.9518 (mp) cc_final: 0.9243 (mp) REVERT: C 136 ASN cc_start: 0.9039 (m110) cc_final: 0.8821 (m-40) REVERT: D 51 ASN cc_start: 0.8422 (t0) cc_final: 0.8107 (t0) REVERT: D 52 MET cc_start: 0.8350 (pmm) cc_final: 0.7953 (tmm) REVERT: D 134 SER cc_start: 0.8740 (t) cc_final: 0.8314 (p) REVERT: D 140 GLU cc_start: 0.7416 (tt0) cc_final: 0.6768 (tt0) REVERT: D 201 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7995 (tt0) REVERT: D 287 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7786 (tm-30) REVERT: D 317 MET cc_start: 0.6654 (mmm) cc_final: 0.6423 (mmp) REVERT: D 637 GLU cc_start: 0.7837 (tt0) cc_final: 0.7225 (tm-30) REVERT: D 641 LEU cc_start: 0.8959 (mt) cc_final: 0.8723 (mp) REVERT: D 651 ARG cc_start: 0.8321 (tmm-80) cc_final: 0.7882 (tmm-80) REVERT: E 59 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8239 (t0) REVERT: E 112 GLU cc_start: 0.8471 (mp0) cc_final: 0.7894 (tp30) REVERT: E 166 PHE cc_start: 0.8478 (m-10) cc_final: 0.8275 (m-10) REVERT: E 349 LEU cc_start: 0.8014 (tp) cc_final: 0.7767 (tp) REVERT: E 629 GLN cc_start: 0.8647 (tt0) cc_final: 0.7455 (tm-30) REVERT: F 51 ASN cc_start: 0.8553 (t0) cc_final: 0.8111 (t0) REVERT: F 146 MET cc_start: 0.5786 (pmm) cc_final: 0.5152 (ppp) REVERT: F 295 TYR cc_start: 0.8258 (m-80) cc_final: 0.6951 (m-80) REVERT: F 317 MET cc_start: 0.6535 (mtm) cc_final: 0.6333 (mtp) REVERT: F 349 LEU cc_start: 0.8226 (tp) cc_final: 0.7839 (tp) REVERT: F 651 ARG cc_start: 0.8424 (ttt180) cc_final: 0.7995 (tmm-80) outliers start: 4 outliers final: 1 residues processed: 569 average time/residue: 0.1865 time to fit residues: 170.5596 Evaluate side-chains 408 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 406 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 188 optimal weight: 0.5980 chunk 324 optimal weight: 1.9990 chunk 335 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 83 optimal weight: 0.0970 chunk 274 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** C 712 GLN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122151 restraints weight = 50718.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121897 restraints weight = 47420.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123713 restraints weight = 42324.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123988 restraints weight = 34605.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124115 restraints weight = 33405.723| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29505 Z= 0.133 Angle : 0.676 9.919 39930 Z= 0.335 Chirality : 0.044 0.191 4626 Planarity : 0.004 0.064 5091 Dihedral : 8.388 165.932 4032 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.91 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.14), residues: 3603 helix: 0.59 (0.15), residues: 1278 sheet: -1.46 (0.21), residues: 600 loop : -2.45 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 270 TYR 0.033 0.001 TYR B 391 PHE 0.026 0.002 PHE D 13 TRP 0.011 0.001 TRP E 519 HIS 0.004 0.001 HIS D 579 Details of bonding type rmsd covalent geometry : bond 0.00301 (29505) covalent geometry : angle 0.67630 (39930) hydrogen bonds : bond 0.03494 ( 907) hydrogen bonds : angle 4.30440 ( 2595) *********************** 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 554 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 1.198 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 387 LEU cc_start: 0.8809 (mt) cc_final: 0.8601 (pt) REVERT: A 400 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6842 (mt-10) REVERT: A 538 SER cc_start: 0.8790 (m) cc_final: 0.8308 (p) REVERT: B 113 ASP cc_start: 0.6911 (t70) cc_final: 0.6699 (t70) REVERT: B 138 ILE cc_start: 0.8411 (tp) cc_final: 0.7837 (tp) REVERT: B 237 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8014 (mmmm) REVERT: B 390 LEU cc_start: 0.9522 (mp) cc_final: 0.9159 (mp) REVERT: C 136 ASN cc_start: 0.9003 (m110) cc_final: 0.8782 (m-40) REVERT: D 51 ASN cc_start: 0.8395 (t0) cc_final: 0.8151 (t0) REVERT: D 52 MET cc_start: 0.8263 (pmm) cc_final: 0.7811 (tmm) REVERT: D 134 SER cc_start: 0.8859 (t) cc_final: 0.8406 (p) REVERT: D 201 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8043 (tt0) REVERT: D 287 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 552 MET cc_start: 0.8182 (tpp) cc_final: 0.7935 (tpt) REVERT: D 637 GLU cc_start: 0.7889 (tt0) cc_final: 0.7262 (tm-30) REVERT: D 641 LEU cc_start: 0.8974 (mt) cc_final: 0.8716 (mp) REVERT: E 92 MET cc_start: 0.7132 (ttm) cc_final: 0.6851 (ttm) REVERT: E 258 GLU cc_start: 0.8696 (pm20) cc_final: 0.8406 (pm20) REVERT: E 629 GLN cc_start: 0.8659 (tt0) cc_final: 0.7446 (tm-30) REVERT: F 51 ASN cc_start: 0.8545 (t0) cc_final: 0.8097 (t0) REVERT: F 60 MET cc_start: 0.7446 (tmm) cc_final: 0.6209 (tmm) REVERT: F 146 MET cc_start: 0.5751 (pmm) cc_final: 0.5212 (ppp) REVERT: F 295 TYR cc_start: 0.8393 (m-80) cc_final: 0.7145 (m-80) REVERT: F 317 MET cc_start: 0.6678 (mtm) cc_final: 0.6466 (mtp) REVERT: F 349 LEU cc_start: 0.8210 (tp) cc_final: 0.7854 (tp) REVERT: F 651 ARG cc_start: 0.8430 (ttt180) cc_final: 0.7922 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.1828 time to fit residues: 164.6050 Evaluate side-chains 413 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 241 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 264 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN C 171 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 GLN E 448 ASN E 560 ASN F 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124608 restraints weight = 51019.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125059 restraints weight = 44972.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126396 restraints weight = 39664.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126817 restraints weight = 32099.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126981 restraints weight = 30476.640| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29505 Z= 0.114 Angle : 0.673 10.513 39930 Z= 0.333 Chirality : 0.044 0.191 4626 Planarity : 0.004 0.064 5091 Dihedral : 8.154 173.220 4032 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.85 % Favored : 89.73 % Rotamer: Outliers : 0.06 % Allowed : 1.18 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.14), residues: 3603 helix: 0.63 (0.15), residues: 1278 sheet: -1.27 (0.21), residues: 597 loop : -2.43 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 654 TYR 0.017 0.001 TYR C 752 PHE 0.023 0.001 PHE B 102 TRP 0.010 0.001 TRP E 248 HIS 0.005 0.001 HIS C 449 Details of bonding type rmsd covalent geometry : bond 0.00247 (29505) covalent geometry : angle 0.67296 (39930) hydrogen bonds : bond 0.03194 ( 907) hydrogen bonds : angle 4.20161 ( 2595) *********************** 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 565 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 563 time to evaluate : 1.227 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 538 SER cc_start: 0.8763 (m) cc_final: 0.8300 (p) REVERT: A 539 ILE cc_start: 0.8458 (tt) cc_final: 0.8163 (tt) REVERT: B 237 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8394 (tppt) REVERT: B 391 TYR cc_start: 0.8263 (t80) cc_final: 0.7965 (t80) REVERT: B 650 LEU cc_start: 0.7137 (mt) cc_final: 0.6747 (mp) REVERT: C 136 ASN cc_start: 0.9007 (m110) cc_final: 0.8790 (m-40) REVERT: D 51 ASN cc_start: 0.8286 (t0) cc_final: 0.8042 (t0) REVERT: D 52 MET cc_start: 0.8250 (pmm) cc_final: 0.7758 (tmm) REVERT: D 134 SER cc_start: 0.8742 (t) cc_final: 0.8198 (p) REVERT: D 201 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8013 (tt0) REVERT: D 287 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D 552 MET cc_start: 0.8208 (tpp) cc_final: 0.7977 (tpt) REVERT: D 637 GLU cc_start: 0.7859 (tt0) cc_final: 0.7144 (tm-30) REVERT: D 641 LEU cc_start: 0.8986 (mt) cc_final: 0.8757 (mp) REVERT: E 112 GLU cc_start: 0.8383 (mp0) cc_final: 0.7686 (tp30) REVERT: E 349 LEU cc_start: 0.7974 (tp) cc_final: 0.7730 (tp) REVERT: E 629 GLN cc_start: 0.8648 (tt0) cc_final: 0.7459 (tm-30) REVERT: F 51 ASN cc_start: 0.8419 (t0) cc_final: 0.8141 (t0) REVERT: F 60 MET cc_start: 0.7378 (tmm) cc_final: 0.6308 (tmm) REVERT: F 146 MET cc_start: 0.5602 (pmm) cc_final: 0.5223 (ppp) REVERT: F 254 ASP cc_start: 0.9162 (m-30) cc_final: 0.8940 (m-30) REVERT: F 295 TYR cc_start: 0.8448 (m-80) cc_final: 0.7157 (m-80) REVERT: F 349 LEU cc_start: 0.8228 (tp) cc_final: 0.7633 (tp) REVERT: F 651 ARG cc_start: 0.8421 (ttt180) cc_final: 0.7894 (tmm-80) outliers start: 2 outliers final: 0 residues processed: 564 average time/residue: 0.1794 time to fit residues: 164.7719 Evaluate side-chains 407 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 317 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 321 optimal weight: 8.9990 chunk 324 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 358 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 136 ASN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119045 restraints weight = 51475.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117661 restraints weight = 49365.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119099 restraints weight = 44533.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119666 restraints weight = 37395.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119914 restraints weight = 34897.470| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29505 Z= 0.172 Angle : 0.730 10.542 39930 Z= 0.363 Chirality : 0.046 0.209 4626 Planarity : 0.005 0.062 5091 Dihedral : 8.154 164.130 4032 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.80 % Favored : 87.73 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.14), residues: 3603 helix: 0.44 (0.15), residues: 1275 sheet: -1.46 (0.21), residues: 606 loop : -2.45 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 32 TYR 0.021 0.002 TYR E 199 PHE 0.028 0.002 PHE F 13 TRP 0.015 0.002 TRP D 292 HIS 0.005 0.001 HIS B 663 Details of bonding type rmsd covalent geometry : bond 0.00394 (29505) covalent geometry : angle 0.72953 (39930) hydrogen bonds : bond 0.03971 ( 907) hydrogen bonds : angle 4.54225 ( 2595) *********************** 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 533 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 1.066 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 538 SER cc_start: 0.8863 (m) cc_final: 0.8419 (p) REVERT: B 113 ASP cc_start: 0.6915 (t70) cc_final: 0.6464 (t70) REVERT: B 201 TYR cc_start: 0.7722 (t80) cc_final: 0.7470 (t80) REVERT: B 289 GLN cc_start: 0.8371 (pp30) cc_final: 0.7537 (pp30) REVERT: B 391 TYR cc_start: 0.8037 (t80) cc_final: 0.7580 (t80) REVERT: B 536 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8483 (mm-40) REVERT: C 136 ASN cc_start: 0.9075 (m110) cc_final: 0.8827 (m-40) REVERT: D 51 ASN cc_start: 0.8455 (t0) cc_final: 0.8215 (t0) REVERT: D 52 MET cc_start: 0.8335 (pmm) cc_final: 0.7876 (tmm) REVERT: D 94 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8698 (mm-40) REVERT: D 134 SER cc_start: 0.8889 (t) cc_final: 0.8477 (p) REVERT: D 245 MET cc_start: 0.8125 (mmm) cc_final: 0.7787 (mmm) REVERT: D 287 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 448 ASN cc_start: 0.7871 (m110) cc_final: 0.7617 (m-40) REVERT: D 521 MET cc_start: 0.8259 (ppp) cc_final: 0.7973 (ppp) REVERT: D 552 MET cc_start: 0.8254 (tpp) cc_final: 0.7971 (tpt) REVERT: D 637 GLU cc_start: 0.7981 (tt0) cc_final: 0.7240 (tm-30) REVERT: D 641 LEU cc_start: 0.9016 (mt) cc_final: 0.8751 (mp) REVERT: E 45 MET cc_start: 0.6950 (mmp) cc_final: 0.5975 (mmp) REVERT: E 112 GLU cc_start: 0.8335 (mp0) cc_final: 0.7851 (tp30) REVERT: E 349 LEU cc_start: 0.8301 (tp) cc_final: 0.8003 (tp) REVERT: E 629 GLN cc_start: 0.8696 (tt0) cc_final: 0.7433 (tm-30) REVERT: E 654 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.7559 (ptp90) REVERT: F 51 ASN cc_start: 0.8555 (t0) cc_final: 0.8163 (t0) REVERT: F 60 MET cc_start: 0.7140 (tmm) cc_final: 0.6114 (tmm) REVERT: F 146 MET cc_start: 0.6116 (pmm) cc_final: 0.5632 (ppp) REVERT: F 295 TYR cc_start: 0.8632 (m-80) cc_final: 0.7515 (m-80) REVERT: F 349 LEU cc_start: 0.8234 (tp) cc_final: 0.7970 (tp) REVERT: F 614 ASN cc_start: 0.7386 (m-40) cc_final: 0.7145 (m-40) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.1806 time to fit residues: 156.5715 Evaluate side-chains 384 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 332 optimal weight: 0.4980 chunk 225 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 251 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 152 optimal weight: 0.4980 chunk 305 optimal weight: 0.1980 chunk 130 optimal weight: 20.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 GLN D 2 ASN E 448 ASN ** E 560 ASN ** 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 = 0.3968 r_free = 0.3968 target = 0.159989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123512 restraints weight = 50213.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123733 restraints weight = 45243.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124625 restraints weight = 40336.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125410 restraints weight = 35518.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125616 restraints weight = 32244.929| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29505 Z= 0.114 Angle : 0.697 10.772 39930 Z= 0.344 Chirality : 0.044 0.203 4626 Planarity : 0.004 0.062 5091 Dihedral : 7.937 172.278 4032 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.58 % Favored : 90.01 % Rotamer: Outliers : 0.03 % Allowed : 0.50 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.14), residues: 3603 helix: 0.57 (0.15), residues: 1275 sheet: -1.25 (0.22), residues: 585 loop : -2.37 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 32 TYR 0.013 0.001 TYR D 199 PHE 0.056 0.002 PHE E 61 TRP 0.013 0.002 TRP E 497 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00248 (29505) covalent geometry : angle 0.69725 (39930) hydrogen bonds : bond 0.03244 ( 907) hydrogen bonds : angle 4.31228 ( 2595) ********************** 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 551 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 550 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 GLN cc_start: 0.8448 (mp10) cc_final: 0.8223 (mp10) REVERT: A 538 SER cc_start: 0.8829 (m) cc_final: 0.8379 (p) REVERT: B 201 TYR cc_start: 0.7643 (t80) cc_final: 0.7274 (t80) REVERT: B 237 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8391 (tppt) REVERT: B 289 GLN cc_start: 0.8401 (pp30) cc_final: 0.7601 (pp30) REVERT: B 391 TYR cc_start: 0.7960 (t80) cc_final: 0.7509 (t80) REVERT: B 536 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8504 (mm-40) REVERT: B 650 LEU cc_start: 0.7047 (mt) cc_final: 0.6660 (mp) REVERT: C 136 ASN cc_start: 0.9056 (m110) cc_final: 0.8818 (m-40) REVERT: C 249 GLN cc_start: 0.8582 (pp30) cc_final: 0.8145 (pp30) REVERT: D 51 ASN cc_start: 0.8293 (t0) cc_final: 0.8067 (t0) REVERT: D 52 MET cc_start: 0.8314 (pmm) cc_final: 0.7818 (tmm) REVERT: D 134 SER cc_start: 0.8770 (t) cc_final: 0.8260 (p) REVERT: D 245 MET cc_start: 0.7973 (mmm) cc_final: 0.7756 (mmm) REVERT: D 287 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8062 (tm-30) REVERT: D 552 MET cc_start: 0.8169 (tpp) cc_final: 0.7904 (tpt) REVERT: D 637 GLU cc_start: 0.7801 (tt0) cc_final: 0.7100 (tm-30) REVERT: D 641 LEU cc_start: 0.8952 (mt) cc_final: 0.8734 (mp) REVERT: E 60 MET cc_start: 0.7493 (ppp) cc_final: 0.6631 (tmm) REVERT: E 112 GLU cc_start: 0.8298 (mp0) cc_final: 0.7870 (tp30) REVERT: E 114 ILE cc_start: 0.8215 (mm) cc_final: 0.7948 (tp) REVERT: E 349 LEU cc_start: 0.8049 (tp) cc_final: 0.7838 (tp) REVERT: E 629 GLN cc_start: 0.8649 (tt0) cc_final: 0.7432 (tm-30) REVERT: F 51 ASN cc_start: 0.8333 (t0) cc_final: 0.7935 (t0) REVERT: F 60 MET cc_start: 0.7182 (tmm) cc_final: 0.6359 (tmm) REVERT: F 146 MET cc_start: 0.6161 (pmm) cc_final: 0.5647 (ppp) REVERT: F 220 MET cc_start: 0.8778 (tpp) cc_final: 0.8547 (tpt) REVERT: F 254 ASP cc_start: 0.9198 (m-30) cc_final: 0.8975 (m-30) REVERT: F 349 LEU cc_start: 0.8256 (tp) cc_final: 0.7976 (tp) outliers start: 1 outliers final: 0 residues processed: 550 average time/residue: 0.1821 time to fit residues: 163.6872 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 : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 69 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 252 optimal weight: 0.0050 chunk 328 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121148 restraints weight = 50903.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120393 restraints weight = 51617.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121933 restraints weight = 47258.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122839 restraints weight = 37214.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122995 restraints weight = 33910.122| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29505 Z= 0.150 Angle : 0.715 10.769 39930 Z= 0.354 Chirality : 0.045 0.193 4626 Planarity : 0.005 0.062 5091 Dihedral : 7.941 168.896 4032 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.46 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.14), residues: 3603 helix: 0.48 (0.15), residues: 1272 sheet: -1.37 (0.21), residues: 600 loop : -2.40 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 222 TYR 0.028 0.001 TYR F 38 PHE 0.020 0.002 PHE E 69 TRP 0.014 0.001 TRP E 292 HIS 0.004 0.001 HIS D 579 Details of bonding type rmsd covalent geometry : bond 0.00346 (29505) covalent geometry : angle 0.71474 (39930) hydrogen bonds : bond 0.03637 ( 907) hydrogen bonds : angle 4.45725 ( 2595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4406.89 seconds wall clock time: 77 minutes 16.31 seconds (4636.31 seconds total)