Starting phenix.real_space_refine on Thu Sep 26 14:15:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/09_2024/7zep_14691.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/09_2024/7zep_14691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/09_2024/7zep_14691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/09_2024/7zep_14691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/09_2024/7zep_14691.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/09_2024/7zep_14691.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.099 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 86 5.16 5 C 8504 2.51 5 N 2320 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13324 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6661 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6661 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2029 SG CYS A 287 52.541 75.712 51.905 1.00 77.66 S ATOM 2306 SG CYS A 321 53.320 76.554 48.500 1.00 56.85 S ATOM 2312 SG CYS A 322 52.404 72.920 49.565 1.00 53.20 S ATOM 8690 SG CYS B 287 71.196 26.443 51.859 1.00 80.24 S ATOM 8967 SG CYS B 321 70.245 25.851 48.220 1.00 56.62 S ATOM 8973 SG CYS B 322 71.189 29.368 49.398 1.00 53.63 S Time building chain proxies: 8.41, per 1000 atoms: 0.63 Number of scatterers: 13324 At special positions: 0 Unit cell: (124.474, 103.554, 126.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 86 16.00 O 2412 8.00 N 2320 7.00 C 8504 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 16 sheets defined 45.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.769A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.608A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.072A pdb=" N ILE A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix removed outlier: 3.626A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.528A pdb=" N LYS A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.567A pdb=" N GLU A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.513A pdb=" N GLN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 482 through 501 Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.667A pdb=" N ILE A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 586 removed outlier: 3.638A pdb=" N ILE A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.658A pdb=" N MET A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 614 " --> pdb=" O MET A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.533A pdb=" N ARG A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 removed outlier: 3.506A pdb=" N LYS A 683 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.839A pdb=" N THR A 707 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 721 Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.752A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.642A pdb=" N GLU A 762 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 763 " --> pdb=" O CYS A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 759 through 763' Processing helix chain 'A' and resid 784 through 803 removed outlier: 3.526A pdb=" N CYS A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.506A pdb=" N TYR A 824 " --> pdb=" O GLU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 877 through 887 removed outlier: 4.004A pdb=" N LEU A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 883 " --> pdb=" O PRO A 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 34 removed outlier: 4.097A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 56 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.595A pdb=" N LYS B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.978A pdb=" N ILE B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 240 removed outlier: 3.520A pdb=" N VAL B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.885A pdb=" N ARG B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.674A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.528A pdb=" N GLN B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 482 through 501 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 543 through 560 removed outlier: 3.539A pdb=" N SER B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 586 removed outlier: 3.627A pdb=" N ILE B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 643 removed outlier: 3.831A pdb=" N ARG B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.845A pdb=" N THR B 707 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 721 Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.818A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.595A pdb=" N GLU B 762 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 763 " --> pdb=" O CYS B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 763' Processing helix chain 'B' and resid 784 through 803 removed outlier: 3.513A pdb=" N MET B 789 " --> pdb=" O VAL B 785 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 790 " --> pdb=" O GLU B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 818 through 831 Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 855 through 858 removed outlier: 3.609A pdb=" N SER B 858 " --> pdb=" O ARG B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 855 through 858' Processing helix chain 'B' and resid 877 through 887 removed outlier: 3.973A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 4.688A pdb=" N VAL A 18 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.717A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 296 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 315 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 298 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N CYS A 313 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 300 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR A 311 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 302 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A 214 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.590A pdb=" N ALA A 323 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.274A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.550A pdb=" N ILE A 627 " --> pdb=" O ARG A 647 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU A 649 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TYR A 629 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 595 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 702 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL A 597 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.291A pdb=" N SER A 863 " --> pdb=" O HIS A 892 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR A 894 " --> pdb=" O SER A 863 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 865 " --> pdb=" O TYR A 894 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N PHE A 896 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY A 867 " --> pdb=" O PHE A 896 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.260A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.572A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 283 through 284 removed outlier: 3.633A pdb=" N ALA B 323 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.316A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.100A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 595 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU B 702 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL B 597 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.233A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1593 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: 4.43 Time building geometry restraints manager: 3.49 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: 4346 1.34 - 1.46: 2830 1.46 - 1.58: 6312 1.58 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 13610 Sorted by residual: bond pdb=" CG PRO B 409 " pdb=" CD PRO B 409 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 8.07e-01 bond pdb=" CG PRO A 409 " pdb=" CD PRO A 409 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 8.00e-01 bond pdb=" CA PRO B 12 " pdb=" C PRO B 12 " ideal model delta sigma weight residual 1.528 1.521 0.008 9.10e-03 1.21e+04 7.11e-01 bond pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 1.520 1.527 -0.007 8.80e-03 1.29e+04 6.75e-01 bond pdb=" CB PRO B 236 " pdb=" CG PRO B 236 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.20e-01 ... (remaining 13605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 17829 1.16 - 2.32: 415 2.32 - 3.47: 103 3.47 - 4.63: 19 4.63 - 5.79: 8 Bond angle restraints: 18374 Sorted by residual: angle pdb=" C GLU B 137 " pdb=" CA GLU B 137 " pdb=" CB GLU B 137 " ideal model delta sigma weight residual 110.42 116.21 -5.79 1.99e+00 2.53e-01 8.47e+00 angle pdb=" C GLU A 137 " pdb=" CA GLU A 137 " pdb=" CB GLU A 137 " ideal model delta sigma weight residual 110.42 116.06 -5.64 1.99e+00 2.53e-01 8.04e+00 angle pdb=" C CYS A 287 " pdb=" N GLN A 288 " pdb=" CA GLN A 288 " ideal model delta sigma weight residual 122.28 126.10 -3.82 1.77e+00 3.19e-01 4.66e+00 angle pdb=" CA GLN A 288 " pdb=" CB GLN A 288 " pdb=" CG GLN A 288 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.26e+00 angle pdb=" CA GLN B 288 " pdb=" CB GLN B 288 " pdb=" CG GLN B 288 " ideal model delta sigma weight residual 114.10 118.14 -4.04 2.00e+00 2.50e-01 4.07e+00 ... (remaining 18369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7506 17.84 - 35.69: 631 35.69 - 53.53: 136 53.53 - 71.38: 28 71.38 - 89.22: 15 Dihedral angle restraints: 8316 sinusoidal: 3484 harmonic: 4832 Sorted by residual: dihedral pdb=" CA ASP A 191 " pdb=" CB ASP A 191 " pdb=" CG ASP A 191 " pdb=" OD1 ASP A 191 " ideal model delta sinusoidal sigma weight residual -30.00 -87.21 57.21 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CG ARG B 406 " pdb=" CD ARG B 406 " pdb=" NE ARG B 406 " pdb=" CZ ARG B 406 " ideal model delta sinusoidal sigma weight residual 180.00 -135.08 -44.92 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ARG B 724 " pdb=" C ARG B 724 " pdb=" N GLU B 725 " pdb=" CA GLU B 725 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 8313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1206 0.027 - 0.054: 522 0.054 - 0.082: 133 0.082 - 0.109: 109 0.109 - 0.136: 48 Chirality restraints: 2018 Sorted by residual: chirality pdb=" CA GLN A 288 " pdb=" N GLN A 288 " pdb=" C GLN A 288 " pdb=" CB GLN A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE B 464 " pdb=" N ILE B 464 " pdb=" C ILE B 464 " pdb=" CB ILE B 464 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 464 " pdb=" N ILE A 464 " pdb=" C ILE A 464 " pdb=" CB ILE A 464 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 2015 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 231 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO B 232 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 288 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO B 289 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 235 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 236 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2031 2.76 - 3.30: 12251 3.30 - 3.83: 21091 3.83 - 4.37: 26288 4.37 - 4.90: 45867 Nonbonded interactions: 107528 Sorted by model distance: nonbonded pdb=" O GLU A 424 " pdb=" ND2 ASN A 428 " model vdw 2.231 3.120 nonbonded pdb=" OD2 ASP A 703 " pdb=" NE2 GLN A 706 " model vdw 2.258 3.120 nonbonded pdb=" OD1 ASP A 191 " pdb=" OH TYR A 245 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 558 " pdb=" OG SER A 566 " model vdw 2.270 3.040 nonbonded pdb=" N ALA B 841 " pdb=" OD2 ASP B 852 " model vdw 2.272 3.120 ... (remaining 107523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.540 Find NCS groups from input model: 0.360 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.002 0.039 13610 Z= 0.136 Angle : 0.475 5.792 18374 Z= 0.259 Chirality : 0.040 0.136 2018 Planarity : 0.004 0.050 2360 Dihedral : 14.255 89.224 5192 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1638 helix: 0.08 (0.20), residues: 642 sheet: 0.57 (0.31), residues: 268 loop : 0.25 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.002 0.000 HIS B 848 PHE 0.013 0.001 PHE B 218 TYR 0.013 0.001 TYR A 629 ARG 0.007 0.000 ARG B 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.588 Fit side-chains REVERT: A 196 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8252 (ttmm) REVERT: A 316 ARG cc_start: 0.7610 (ttt90) cc_final: 0.7184 (tpt170) REVERT: A 621 HIS cc_start: 0.7936 (m-70) cc_final: 0.7514 (m170) REVERT: B 710 LEU cc_start: 0.8069 (mt) cc_final: 0.7842 (mt) REVERT: B 852 ASP cc_start: 0.7055 (m-30) cc_final: 0.6643 (m-30) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3015 time to fit residues: 76.9526 Evaluate side-chains 150 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 128 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 592 ASN A 706 GLN A 787 GLN B 706 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13610 Z= 0.193 Angle : 0.519 6.984 18374 Z= 0.272 Chirality : 0.043 0.141 2018 Planarity : 0.004 0.047 2360 Dihedral : 3.671 16.010 1824 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.54 % Allowed : 4.88 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1638 helix: 0.89 (0.20), residues: 656 sheet: 0.53 (0.30), residues: 270 loop : 0.34 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.002 0.001 HIS A 285 PHE 0.015 0.001 PHE A 218 TYR 0.013 0.001 TYR B 629 ARG 0.005 0.000 ARG B 643 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8031 (ttmt) REVERT: A 621 HIS cc_start: 0.7979 (m-70) cc_final: 0.7577 (m170) REVERT: A 658 ASN cc_start: 0.7100 (p0) cc_final: 0.6701 (m110) REVERT: B 229 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6905 (ptt90) REVERT: B 610 MET cc_start: 0.7787 (mtp) cc_final: 0.7534 (mtm) REVERT: B 710 LEU cc_start: 0.8063 (mt) cc_final: 0.7861 (mt) REVERT: B 787 GLN cc_start: 0.8463 (mt0) cc_final: 0.8250 (mt0) REVERT: B 824 TYR cc_start: 0.7480 (t80) cc_final: 0.7219 (t80) REVERT: B 852 ASP cc_start: 0.6816 (m-30) cc_final: 0.6561 (m-30) outliers start: 8 outliers final: 5 residues processed: 175 average time/residue: 0.2677 time to fit residues: 67.7763 Evaluate side-chains 155 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 123 optimal weight: 0.0570 chunk 101 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 147 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 224 GLN A 618 ASN A 787 GLN B 217 GLN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13610 Z= 0.146 Angle : 0.465 6.805 18374 Z= 0.240 Chirality : 0.041 0.141 2018 Planarity : 0.004 0.040 2360 Dihedral : 3.588 15.420 1824 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.61 % Allowed : 7.11 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1638 helix: 1.40 (0.20), residues: 652 sheet: 0.47 (0.31), residues: 270 loop : 0.27 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.001 0.000 HIS B 848 PHE 0.014 0.001 PHE A 218 TYR 0.011 0.001 TYR B 629 ARG 0.007 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 1.722 Fit side-chains REVERT: A 196 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8170 (ttmm) REVERT: A 225 GLU cc_start: 0.6561 (tm-30) cc_final: 0.5656 (tm-30) REVERT: A 229 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7757 (mtm110) REVERT: A 621 HIS cc_start: 0.7902 (m-70) cc_final: 0.7551 (m170) REVERT: A 780 LYS cc_start: 0.7545 (mttt) cc_final: 0.7171 (mmtt) REVERT: B 229 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6754 (ptt90) REVERT: B 710 LEU cc_start: 0.8073 (mt) cc_final: 0.7866 (mt) outliers start: 9 outliers final: 6 residues processed: 166 average time/residue: 0.2905 time to fit residues: 69.0909 Evaluate side-chains 159 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN A 661 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13610 Z= 0.277 Angle : 0.516 6.700 18374 Z= 0.265 Chirality : 0.043 0.137 2018 Planarity : 0.004 0.038 2360 Dihedral : 3.765 17.163 1824 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.36 % Allowed : 8.54 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1638 helix: 1.37 (0.20), residues: 648 sheet: 0.32 (0.30), residues: 270 loop : 0.26 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.005 0.001 HIS A 625 PHE 0.016 0.001 PHE A 218 TYR 0.015 0.001 TYR B 629 ARG 0.008 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8121 (ttmm) REVERT: A 311 TYR cc_start: 0.7171 (m-80) cc_final: 0.6879 (m-80) REVERT: A 548 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: A 621 HIS cc_start: 0.7948 (m-70) cc_final: 0.7612 (m170) REVERT: A 780 LYS cc_start: 0.7589 (mttt) cc_final: 0.7198 (mmtt) REVERT: B 119 ARG cc_start: 0.8315 (mtm180) cc_final: 0.6654 (mtp-110) REVERT: B 229 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6775 (ptt90) REVERT: B 314 MET cc_start: 0.8364 (mtt) cc_final: 0.7983 (mtm) REVERT: B 548 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: B 710 LEU cc_start: 0.8067 (mt) cc_final: 0.7863 (mt) REVERT: B 729 ARG cc_start: 0.7399 (mpt180) cc_final: 0.7131 (mmt90) REVERT: B 852 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7121 (m-30) outliers start: 20 outliers final: 12 residues processed: 173 average time/residue: 0.3000 time to fit residues: 73.2290 Evaluate side-chains 172 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 0.0010 chunk 142 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 86 GLN B 592 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13610 Z= 0.195 Angle : 0.482 6.925 18374 Z= 0.247 Chirality : 0.042 0.138 2018 Planarity : 0.004 0.037 2360 Dihedral : 3.692 16.701 1824 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.42 % Allowed : 9.28 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1638 helix: 1.51 (0.20), residues: 648 sheet: 0.27 (0.31), residues: 270 loop : 0.30 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.005 0.001 HIS A 625 PHE 0.013 0.001 PHE A 218 TYR 0.013 0.001 TYR B 629 ARG 0.009 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.456 Fit side-chains REVERT: A 196 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8094 (ttmm) REVERT: A 217 GLN cc_start: 0.7145 (tp-100) cc_final: 0.6936 (tp40) REVERT: A 225 GLU cc_start: 0.6607 (tm-30) cc_final: 0.4835 (tm-30) REVERT: A 229 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7615 (ptt90) REVERT: A 311 TYR cc_start: 0.7163 (m-80) cc_final: 0.6856 (m-80) REVERT: A 676 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: A 780 LYS cc_start: 0.7581 (mttt) cc_final: 0.7203 (mmtt) REVERT: B 119 ARG cc_start: 0.8291 (mtm180) cc_final: 0.6656 (mtp-110) REVERT: B 229 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6559 (ptt90) REVERT: B 233 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: B 548 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: B 710 LEU cc_start: 0.8081 (mt) cc_final: 0.7876 (mt) REVERT: B 729 ARG cc_start: 0.7393 (mpt180) cc_final: 0.7157 (mmt90) REVERT: B 789 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8360 (mmp) REVERT: B 852 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.7011 (m-30) outliers start: 21 outliers final: 12 residues processed: 178 average time/residue: 0.2854 time to fit residues: 71.6292 Evaluate side-chains 177 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13610 Z= 0.197 Angle : 0.479 6.734 18374 Z= 0.245 Chirality : 0.042 0.138 2018 Planarity : 0.004 0.039 2360 Dihedral : 3.653 16.593 1824 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.83 % Allowed : 8.94 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1638 helix: 1.58 (0.20), residues: 652 sheet: 0.23 (0.30), residues: 270 loop : 0.37 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.004 0.001 HIS A 625 PHE 0.013 0.001 PHE A 218 TYR 0.013 0.001 TYR B 629 ARG 0.009 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8064 (ttmm) REVERT: A 478 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6954 (pm20) REVERT: A 548 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: A 676 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: A 780 LYS cc_start: 0.7575 (mttt) cc_final: 0.7207 (mmtt) REVERT: B 119 ARG cc_start: 0.8289 (mtm180) cc_final: 0.6656 (mtp-110) REVERT: B 229 ARG cc_start: 0.7127 (mtm110) cc_final: 0.6432 (ptt90) REVERT: B 233 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7224 (pm20) REVERT: B 548 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6693 (mt-10) REVERT: B 729 ARG cc_start: 0.7396 (mpt180) cc_final: 0.7173 (mmt90) REVERT: B 852 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.7023 (m-30) outliers start: 27 outliers final: 15 residues processed: 187 average time/residue: 0.2805 time to fit residues: 74.1975 Evaluate side-chains 185 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 158 optimal weight: 0.0050 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13610 Z= 0.206 Angle : 0.488 7.082 18374 Z= 0.249 Chirality : 0.042 0.138 2018 Planarity : 0.004 0.041 2360 Dihedral : 3.651 16.586 1824 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.96 % Allowed : 9.21 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1638 helix: 1.58 (0.20), residues: 652 sheet: 0.20 (0.30), residues: 270 loop : 0.36 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.004 0.001 HIS A 625 PHE 0.012 0.001 PHE A 218 TYR 0.013 0.001 TYR B 629 ARG 0.011 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 288 GLN cc_start: 0.7225 (tp-100) cc_final: 0.6989 (mm-40) REVERT: A 478 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: A 676 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: A 780 LYS cc_start: 0.7562 (mttt) cc_final: 0.7195 (mmtt) REVERT: B 119 ARG cc_start: 0.8250 (mtm180) cc_final: 0.6655 (mtp-110) REVERT: B 217 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6980 (tp-100) REVERT: B 229 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6430 (ptt90) REVERT: B 233 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: B 548 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: B 725 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6648 (tp30) REVERT: B 729 ARG cc_start: 0.7416 (mpt180) cc_final: 0.7200 (mmt90) REVERT: B 852 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.7031 (m-30) outliers start: 29 outliers final: 19 residues processed: 190 average time/residue: 0.2629 time to fit residues: 71.2908 Evaluate side-chains 192 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 638 ASN A 787 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13610 Z= 0.253 Angle : 0.510 7.000 18374 Z= 0.260 Chirality : 0.043 0.136 2018 Planarity : 0.004 0.040 2360 Dihedral : 3.736 17.228 1824 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.96 % Allowed : 9.55 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1638 helix: 1.49 (0.20), residues: 652 sheet: 0.16 (0.30), residues: 270 loop : 0.30 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 413 HIS 0.005 0.001 HIS A 625 PHE 0.012 0.001 PHE A 218 TYR 0.015 0.001 TYR B 629 ARG 0.010 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.554 Fit side-chains REVERT: A 229 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7579 (ptt90) REVERT: A 478 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7019 (pt0) REVERT: A 548 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: A 676 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: A 780 LYS cc_start: 0.7651 (mttt) cc_final: 0.7256 (mmtt) REVERT: A 852 ASP cc_start: 0.7449 (t0) cc_final: 0.7173 (m-30) REVERT: B 119 ARG cc_start: 0.8266 (mtm180) cc_final: 0.6651 (mtp-110) REVERT: B 217 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6982 (tp-100) REVERT: B 229 ARG cc_start: 0.7174 (mtm110) cc_final: 0.6496 (ptt90) REVERT: B 233 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: B 382 TYR cc_start: 0.7931 (m-10) cc_final: 0.7718 (m-80) REVERT: B 548 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: B 729 ARG cc_start: 0.7462 (mpt180) cc_final: 0.7246 (mmt90) REVERT: B 852 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7133 (m-30) outliers start: 29 outliers final: 20 residues processed: 190 average time/residue: 0.2790 time to fit residues: 75.8389 Evaluate side-chains 194 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 138 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 787 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13610 Z= 0.170 Angle : 0.479 7.236 18374 Z= 0.242 Chirality : 0.041 0.139 2018 Planarity : 0.003 0.036 2360 Dihedral : 3.632 16.255 1824 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.83 % Allowed : 9.69 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1638 helix: 1.65 (0.20), residues: 652 sheet: 0.20 (0.30), residues: 270 loop : 0.37 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 413 HIS 0.004 0.000 HIS A 625 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR B 629 ARG 0.009 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: A 548 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: A 553 SER cc_start: 0.7909 (m) cc_final: 0.7687 (p) REVERT: A 621 HIS cc_start: 0.7777 (m-70) cc_final: 0.7352 (m170) REVERT: A 780 LYS cc_start: 0.7635 (mttt) cc_final: 0.7234 (mmtt) REVERT: A 852 ASP cc_start: 0.7391 (t0) cc_final: 0.7143 (m-30) REVERT: B 119 ARG cc_start: 0.8256 (mtm180) cc_final: 0.6662 (mtp-110) REVERT: B 217 GLN cc_start: 0.7188 (mm110) cc_final: 0.6967 (tp-100) REVERT: B 229 ARG cc_start: 0.6960 (mtm110) cc_final: 0.6285 (ptt90) REVERT: B 233 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: B 272 ARG cc_start: 0.7818 (ptm160) cc_final: 0.7426 (mtp180) REVERT: B 382 TYR cc_start: 0.7930 (m-10) cc_final: 0.7714 (m-80) REVERT: B 548 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: B 729 ARG cc_start: 0.7427 (mpt180) cc_final: 0.7171 (mmt90) REVERT: B 787 GLN cc_start: 0.8712 (mt0) cc_final: 0.8453 (mt0) REVERT: B 852 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6954 (m-30) outliers start: 27 outliers final: 19 residues processed: 192 average time/residue: 0.2657 time to fit residues: 73.2112 Evaluate side-chains 191 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 163 optimal weight: 0.2980 chunk 150 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 GLN B 848 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13610 Z= 0.165 Angle : 0.483 7.166 18374 Z= 0.246 Chirality : 0.041 0.161 2018 Planarity : 0.003 0.036 2360 Dihedral : 3.575 16.004 1824 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.83 % Allowed : 9.69 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1638 helix: 1.70 (0.20), residues: 652 sheet: 0.25 (0.31), residues: 270 loop : 0.38 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.004 0.000 HIS A 625 PHE 0.010 0.001 PHE A 218 TYR 0.018 0.001 TYR B 824 ARG 0.009 0.000 ARG B 690 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.462 Fit side-chains REVERT: A 478 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: A 548 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6555 (mt-10) REVERT: A 553 SER cc_start: 0.7912 (m) cc_final: 0.7692 (p) REVERT: A 621 HIS cc_start: 0.7693 (m-70) cc_final: 0.7367 (m90) REVERT: A 676 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: A 780 LYS cc_start: 0.7613 (mttt) cc_final: 0.7237 (mmtt) REVERT: A 852 ASP cc_start: 0.7390 (t0) cc_final: 0.7154 (m-30) REVERT: B 119 ARG cc_start: 0.8276 (mtm180) cc_final: 0.6663 (mtp-110) REVERT: B 229 ARG cc_start: 0.7052 (mtm110) cc_final: 0.6354 (ptt90) REVERT: B 233 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: B 272 ARG cc_start: 0.7897 (ptm160) cc_final: 0.7457 (mtp180) REVERT: B 548 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: B 729 ARG cc_start: 0.7410 (mpt180) cc_final: 0.7163 (mmt90) REVERT: B 787 GLN cc_start: 0.8684 (mt0) cc_final: 0.8392 (mt0) outliers start: 27 outliers final: 20 residues processed: 185 average time/residue: 0.2670 time to fit residues: 71.4692 Evaluate side-chains 192 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 0.0470 chunk 39 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 19 optimal weight: 0.0470 chunk 36 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 787 GLN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129919 restraints weight = 14821.561| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.44 r_work: 0.3280 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13610 Z= 0.150 Angle : 0.472 7.105 18374 Z= 0.239 Chirality : 0.041 0.160 2018 Planarity : 0.003 0.035 2360 Dihedral : 3.508 15.501 1824 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.69 % Allowed : 9.76 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.21), residues: 1638 helix: 1.80 (0.21), residues: 652 sheet: 0.30 (0.31), residues: 270 loop : 0.40 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 413 HIS 0.004 0.000 HIS A 625 PHE 0.010 0.001 PHE A 207 TYR 0.012 0.001 TYR A 311 ARG 0.009 0.000 ARG B 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.43 seconds wall clock time: 50 minutes 36.52 seconds (3036.52 seconds total)