Starting phenix.real_space_refine on Mon Sep 30 06:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/09_2024/8dev_27400.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/09_2024/8dev_27400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/09_2024/8dev_27400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/09_2024/8dev_27400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/09_2024/8dev_27400.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/09_2024/8dev_27400.cif" } resolution = 3.08 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= -0.000 sd= 0.044 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 P 19 5.49 5 S 135 5.16 5 C 15631 2.51 5 N 3920 2.21 5 O 4540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24245 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7761 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 39, 'TRANS': 997} Chain breaks: 1 Chain: "B" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 7813 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 40, 'TRANS': 1002} Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7806 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 40, 'TRANS': 1001} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'RE6': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="RE6 D 1 " pdbres="DAB D 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DAB:plan-1': 4, 'RE6:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 37 Classifications: {'peptide': 5} Modifications used: {'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DAB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 304 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 15.49, per 1000 atoms: 0.64 Number of scatterers: 24245 At special positions: 0 Unit cell: (130.152, 158.202, 126.786, 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) S 135 16.00 P 19 15.00 O 4540 8.00 N 3920 7.00 C 15631 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 3.1 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DLE D 7 " Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 23 sheets defined 56.6% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.944A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.787A pdb=" N GLU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.533A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.678A pdb=" N THR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 328 through 358 Processing helix chain 'A' and resid 363 through 385 removed outlier: 3.518A pdb=" N THR A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 390 through 421 removed outlier: 3.921A pdb=" N MET A 396 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 452 removed outlier: 5.443A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 removed outlier: 3.628A pdb=" N MET A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 461 through 494 removed outlier: 3.921A pdb=" N TYR A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.793A pdb=" N LYS A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.724A pdb=" N THR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 634 through 637 removed outlier: 3.983A pdb=" N SER A 637 " --> pdb=" O ALA A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 638 through 654 Processing helix chain 'A' and resid 687 through 704 removed outlier: 3.741A pdb=" N LEU A 691 " --> pdb=" O GLY A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 740 through 752 removed outlier: 4.232A pdb=" N LEU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 778 removed outlier: 4.250A pdb=" N MET A 778 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 removed outlier: 3.607A pdb=" N ILE A 783 " --> pdb=" O PRO A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 833 through 848 removed outlier: 3.517A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 865 removed outlier: 3.878A pdb=" N GLU A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 890 removed outlier: 3.688A pdb=" N LEU A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.920A pdb=" N VAL A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 924 removed outlier: 4.071A pdb=" N GLY A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 958 removed outlier: 3.669A pdb=" N ALA A 947 " --> pdb=" O MET A 943 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 998 removed outlier: 3.807A pdb=" N LEU A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Proline residue: A 995 - end of helix removed outlier: 3.556A pdb=" N ILE A 998 " --> pdb=" O VAL A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1041 removed outlier: 4.127A pdb=" N GLN A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix removed outlier: 3.778A pdb=" N LYS A1041 " --> pdb=" O ARG A1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.515A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.972A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 118 removed outlier: 5.494A pdb=" N SER B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.616A pdb=" N THR B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 328 through 358 removed outlier: 3.797A pdb=" N GLU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 385 Proline residue: B 371 - end of helix removed outlier: 3.532A pdb=" N GLY B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 422 removed outlier: 4.279A pdb=" N GLY B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 452 removed outlier: 5.447A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 457 removed outlier: 4.195A pdb=" N PHE B 457 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 495 removed outlier: 3.971A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Proline residue: B 488 - end of helix removed outlier: 3.609A pdb=" N LEU B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 533 removed outlier: 3.717A pdb=" N ARG B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 removed outlier: 3.516A pdb=" N ARG B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 3.902A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 598 No H-bonds generated for 'chain 'B' and resid 596 through 598' Processing helix chain 'B' and resid 628 through 633 removed outlier: 3.669A pdb=" N THR B 633 " --> pdb=" O ASN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.679A pdb=" N GLY B 652 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.749A pdb=" N LEU B 691 " --> pdb=" O GLY B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.705A pdb=" N GLN B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 751 removed outlier: 3.658A pdb=" N ARG B 744 " --> pdb=" O PHE B 740 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 751 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 777 removed outlier: 3.668A pdb=" N ARG B 777 " --> pdb=" O GLY B 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 774 through 777' Processing helix chain 'B' and resid 779 through 783 removed outlier: 3.624A pdb=" N ILE B 783 " --> pdb=" O PRO B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 848 removed outlier: 3.500A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.905A pdb=" N LYS B 865 " --> pdb=" O ARG B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 890 Processing helix chain 'B' and resid 893 through 900 removed outlier: 3.774A pdb=" N ALA B 897 " --> pdb=" O SER B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.677A pdb=" N GLY B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 962 Processing helix chain 'B' and resid 966 through 994 removed outlier: 4.914A pdb=" N ARG B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Proline residue: B 981 - end of helix Processing helix chain 'B' and resid 995 through 998 removed outlier: 3.547A pdb=" N ILE B 998 " --> pdb=" O PRO B 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 995 through 998' Processing helix chain 'B' and resid 1005 through 1040 removed outlier: 3.970A pdb=" N THR B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.538A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.536A pdb=" N ILE C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 148 through 166 removed outlier: 4.601A pdb=" N VAL C 161 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Proline residue: C 162 - end of helix removed outlier: 3.648A pdb=" N ARG C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 296 through 312 Processing helix chain 'C' and resid 329 through 358 Processing helix chain 'C' and resid 363 through 385 Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 404 through 422 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.673A pdb=" N LYS C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 452 removed outlier: 3.767A pdb=" N VAL C 450 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 456 Processing helix chain 'C' and resid 459 through 494 removed outlier: 3.869A pdb=" N THR C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Proline residue: C 488 - end of helix Processing helix chain 'C' and resid 508 through 532 removed outlier: 3.502A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 555 Processing helix chain 'C' and resid 580 through 596 removed outlier: 3.812A pdb=" N THR C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 654 Processing helix chain 'C' and resid 687 through 703 removed outlier: 4.058A pdb=" N LEU C 691 " --> pdb=" O GLY C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 740 through 751 removed outlier: 4.389A pdb=" N LEU C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 785 Processing helix chain 'C' and resid 833 through 849 removed outlier: 3.860A pdb=" N ALA C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 866 removed outlier: 4.330A pdb=" N GLU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 890 removed outlier: 3.840A pdb=" N ALA C 872 " --> pdb=" O SER C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 899 Processing helix chain 'C' and resid 901 through 924 removed outlier: 3.517A pdb=" N GLY C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 962 removed outlier: 3.829A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 998 removed outlier: 5.254A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix removed outlier: 3.559A pdb=" N PHE C 989 " --> pdb=" O THR C 985 " (cutoff:3.500A) Proline residue: C 995 - end of helix Processing helix chain 'C' and resid 1003 through 1040 removed outlier: 4.302A pdb=" N GLN C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 8.070A pdb=" N SER A 87 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA A 82 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER A 89 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR A 80 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET A 78 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 93 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N GLN A 812 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLU A 823 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 814 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 714 " --> pdb=" O SER A 825 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 8.070A pdb=" N SER A 87 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA A 82 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER A 89 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR A 80 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET A 78 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 93 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N GLN A 812 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLU A 823 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 814 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 676 " --> pdb=" O GLY A 826 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 175 removed outlier: 6.497A pdb=" N MET A 287 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE A 139 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 289 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU A 137 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP A 326 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A 139 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 270 removed outlier: 7.987A pdb=" N ARG A 180 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N MET A 769 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET A 182 " --> pdb=" O MET A 769 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLN A 771 " --> pdb=" O MET A 182 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 184 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN A 766 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 758 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 768 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 4.144A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.661A pdb=" N ILE A 258 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 809 removed outlier: 9.136A pdb=" N THR C 233 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 724 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 removed outlier: 7.762A pdb=" N SER B 87 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA B 82 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER B 89 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR B 80 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 78 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 93 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 12.642A pdb=" N GLN B 812 " --> pdb=" O GLU B 823 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N GLU B 823 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 814 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 821 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.762A pdb=" N SER B 87 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA B 82 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER B 89 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR B 80 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 78 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 93 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 12.642A pdb=" N GLN B 812 " --> pdb=" O GLU B 823 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N GLU B 823 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 814 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 821 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 175 removed outlier: 3.568A pdb=" N MET B 138 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU B 291 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE B 136 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 175 removed outlier: 3.540A pdb=" N THR B 284 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR B 277 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 276 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 269 removed outlier: 3.668A pdb=" N ARG B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 757 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 770 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TYR B 755 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 215 through 217 removed outlier: 4.148A pdb=" N GLY B 215 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 232 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR B 231 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE C 726 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 233 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE C 728 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.780A pdb=" N ILE B 258 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 721 through 723 Processing sheet with id=AB8, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AB9, first strand: chain 'B' and resid 788 through 789 Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.953A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.019A pdb=" N GLN C 812 " --> pdb=" O GLU C 823 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N GLU C 823 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL C 814 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 821 " --> pdb=" O VAL C 814 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 826 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 173 removed outlier: 6.603A pdb=" N THR C 285 " --> pdb=" O MET C 141 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET C 141 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET C 287 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE C 139 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 289 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LEU C 137 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP C 326 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE C 139 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 264 through 270 removed outlier: 8.614A pdb=" N ARG C 180 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG C 767 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 757 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 248 through 251 removed outlier: 6.558A pdb=" N ILE C 258 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.514A pdb=" N SER C 608 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 603 " --> pdb=" O ILE C 625 " (cutoff:3.500A) 1467 hydrogen bonds defined for protein. 4263 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: 10.59 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3893 1.31 - 1.43: 5929 1.43 - 1.56: 14515 1.56 - 1.68: 38 1.68 - 1.81: 267 Bond restraints: 24642 Sorted by residual: bond pdb=" C DAB D 4 " pdb=" N DAB D 5 " ideal model delta sigma weight residual 1.329 1.457 -0.128 1.40e-02 5.10e+03 8.38e+01 bond pdb=" C DAB D 9 " pdb=" N DAB D 10 " ideal model delta sigma weight residual 1.329 1.456 -0.127 1.40e-02 5.10e+03 8.21e+01 bond pdb=" C LEU D 8 " pdb=" N DAB D 9 " ideal model delta sigma weight residual 1.329 1.456 -0.127 1.40e-02 5.10e+03 8.19e+01 bond pdb=" C DAB D 10 " pdb=" N THR D 11 " ideal model delta sigma weight residual 1.329 1.454 -0.125 1.40e-02 5.10e+03 7.93e+01 bond pdb=" C THR D 3 " pdb=" N DAB D 4 " ideal model delta sigma weight residual 1.329 1.453 -0.124 1.40e-02 5.10e+03 7.88e+01 ... (remaining 24637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 32815 3.52 - 7.03: 352 7.03 - 10.55: 61 10.55 - 14.06: 1 14.06 - 17.58: 19 Bond angle restraints: 33248 Sorted by residual: angle pdb=" O11 PTY A1106 " pdb=" P1 PTY A1106 " pdb=" O14 PTY A1106 " ideal model delta sigma weight residual 92.90 110.48 -17.58 3.00e+00 1.11e-01 3.43e+01 angle pdb=" N VAL A 968 " pdb=" CA VAL A 968 " pdb=" C VAL A 968 " ideal model delta sigma weight residual 113.53 107.83 5.70 9.80e-01 1.04e+00 3.38e+01 angle pdb=" O11 PTY C1103 " pdb=" P1 PTY C1103 " pdb=" O14 PTY C1103 " ideal model delta sigma weight residual 92.90 109.91 -17.01 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O11 PTY C1102 " pdb=" P1 PTY C1102 " pdb=" O14 PTY C1102 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O11 PTY B1105 " pdb=" P1 PTY B1105 " pdb=" O14 PTY B1105 " ideal model delta sigma weight residual 92.90 109.61 -16.71 3.00e+00 1.11e-01 3.10e+01 ... (remaining 33243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 14401 33.46 - 66.92: 395 66.92 - 100.38: 55 100.38 - 133.84: 14 133.84 - 167.29: 8 Dihedral angle restraints: 14873 sinusoidal: 5969 harmonic: 8904 Sorted by residual: dihedral pdb=" CA PRO C 221 " pdb=" C PRO C 221 " pdb=" N ALA C 222 " pdb=" CA ALA C 222 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" C3 PTY C1101 " pdb=" O11 PTY C1101 " pdb=" P1 PTY C1101 " pdb=" O12 PTY C1101 " ideal model delta sinusoidal sigma weight residual 300.23 132.94 167.29 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3 PTY C1106 " pdb=" O11 PTY C1106 " pdb=" P1 PTY C1106 " pdb=" O12 PTY C1106 " ideal model delta sinusoidal sigma weight residual -59.77 107.25 -167.02 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 14870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2525 0.031 - 0.062: 921 0.062 - 0.094: 266 0.094 - 0.125: 146 0.125 - 0.156: 4 Chirality restraints: 3862 Sorted by residual: chirality pdb=" CA DAB D 9 " pdb=" N DAB D 9 " pdb=" C DAB D 9 " pdb=" CB DAB D 9 " both_signs ideal model delta sigma weight residual False 2.48 2.64 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA LEU C 220 " pdb=" N LEU C 220 " pdb=" C LEU C 220 " pdb=" CB LEU C 220 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE B 498 " pdb=" N ILE B 498 " pdb=" C ILE B 498 " pdb=" CB ILE B 498 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 3859 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 994 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 995 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 995 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 995 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 796 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO B 797 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 797 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 797 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 220 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO C 221 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.026 5.00e-02 4.00e+02 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 156 2.57 - 3.15: 20201 3.15 - 3.74: 34068 3.74 - 4.32: 47898 4.32 - 4.90: 84440 Nonbonded interactions: 186763 Sorted by model distance: nonbonded pdb=" OE1 GLU B 58 " pdb=" OG SER B 813 " model vdw 1.991 3.040 nonbonded pdb=" O LYS B 627 " pdb=" NH1 ARG B 632 " model vdw 2.043 3.120 nonbonded pdb=" OG SER A 148 " pdb=" OE1 GLU A 151 " model vdw 2.055 3.040 nonbonded pdb=" OH TYR A 542 " pdb=" O LEU A 900 " model vdw 2.055 3.040 nonbonded pdb=" OH TYR B 465 " pdb=" OE1 GLN B 936 " model vdw 2.056 3.040 ... (remaining 186758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1042 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C5 or name C6 or name C8 or name N1 or name O10 \ or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O \ 7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C2 or name C20 or name C5 or name C6 or name C8 or name N1 or name O10 or name O \ 11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or resid 1103 or (resid 1104 and (name C1 or name C11 or name C12 or name \ C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1105 and (name \ C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C5 or name C6 o \ r name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 \ or name O30 or name O4 or name O7 or name P1 )) or (resid 1107 and (name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C8 or name O10 or name \ O7 )))) selection = (chain 'B' and (resid 1 through 498 or resid 508 through 1042 or (resid 1102 and \ (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C5 or name C6 or name C \ 8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name \ O30 or name O4 or name O7 or name P1 )) or (resid 1103 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C2 or name C20 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or n \ ame O4 or name O7 or name P1 )) or (resid 1104 and (name C11 or name C12 or name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C8 )) or (resid 1105 and (name C1 or name C11 or name C12 or name C2 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C5 or name C6 or na \ me C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or \ name O30 or name O4 or name O7 or name P1 )) or (resid 1106 and (name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C5 or name C6 or name C8 \ or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O \ 30 or name O4 or name O7 or name P1 )) or (resid 1108 and (name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C20 or name C21 or name C22 or name C8 or name O10 or name O7 )))) selection = (chain 'C' and (resid 1 through 498 or resid 508 through 1042 or (resid 1102 and \ (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C5 or name C6 or name C \ 8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name \ O30 or name O4 or name O7 or name P1 )) or (resid 1103 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C2 or name C20 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or n \ ame O4 or name O7 or name P1 )) or (resid 1104 and (name C11 or name C12 or name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C8 )) or (resid 1105 and (name C1 or name C11 or name C12 or name C20 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C30 or name C31 or name C32 or name C33 or name C5 or name C6 or name C8 \ or name O10 or name O30 or name O4 or name O7 )) or resid 1106 or resid 1108)) } 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: 0.010 Normalize map: mean=0, sd=1: 19.640 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 57.870 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.006 0.128 24642 Z= 0.345 Angle : 0.905 17.576 33248 Z= 0.390 Chirality : 0.039 0.156 3862 Planarity : 0.004 0.100 4158 Dihedral : 16.803 167.294 9167 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.81 (0.16), residues: 3114 helix: 2.15 (0.13), residues: 1655 sheet: -0.37 (0.26), residues: 423 loop : -1.82 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1016 HIS 0.002 0.001 HIS A 688 PHE 0.011 0.001 PHE C1015 TYR 0.015 0.001 TYR B 49 ARG 0.006 0.000 ARG C 767 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 309 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 THR cc_start: 0.8620 (t) cc_final: 0.8362 (m) REVERT: B 984 MET cc_start: 0.8874 (mtp) cc_final: 0.8654 (mtp) REVERT: D 8 LEU cc_start: 0.3480 (OUTLIER) cc_final: 0.3153 (mp) outliers start: 4 outliers final: 0 residues processed: 312 average time/residue: 0.3713 time to fit residues: 187.1393 Evaluate side-chains 259 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 0.0010 chunk 181 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN A 684 ASN A 963 GLN B 135 ASN B 165 GLN B 729 ASN B 859 GLN C 672 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24642 Z= 0.268 Angle : 0.595 6.638 33248 Z= 0.307 Chirality : 0.044 0.190 3862 Planarity : 0.004 0.069 4158 Dihedral : 15.500 164.583 3942 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.16 % Allowed : 6.28 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.84 (0.16), residues: 3114 helix: 2.01 (0.13), residues: 1656 sheet: 0.09 (0.26), residues: 421 loop : -1.72 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 892 HIS 0.002 0.001 HIS A 688 PHE 0.013 0.001 PHE C1015 TYR 0.021 0.002 TYR B 49 ARG 0.006 0.001 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 267 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: A 702 MET cc_start: 0.8149 (mtp) cc_final: 0.7922 (mtp) REVERT: A 843 LYS cc_start: 0.8372 (tmmt) cc_final: 0.7947 (pttp) REVERT: B 152 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8656 (mtp) REVERT: B 862 GLU cc_start: 0.7136 (pm20) cc_final: 0.6549 (pm20) REVERT: C 783 ILE cc_start: 0.8738 (tp) cc_final: 0.8516 (tp) outliers start: 29 outliers final: 18 residues processed: 285 average time/residue: 0.3702 time to fit residues: 167.1982 Evaluate side-chains 271 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 252 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 282 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 280 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 226 GLN A 681 GLN B 729 ASN C 672 ASN C 700 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24642 Z= 0.165 Angle : 0.512 6.142 33248 Z= 0.265 Chirality : 0.041 0.143 3862 Planarity : 0.004 0.059 4158 Dihedral : 14.157 163.390 3940 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.64 % Allowed : 8.36 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 (0.16), residues: 3114 helix: 2.18 (0.13), residues: 1661 sheet: 0.43 (0.26), residues: 423 loop : -1.53 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.003 0.000 HIS C 688 PHE 0.013 0.001 PHE C1015 TYR 0.015 0.001 TYR B 49 ARG 0.007 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 272 time to evaluate : 2.494 Fit side-chains revert: symmetry clash REVERT: B 135 ASN cc_start: 0.7457 (m-40) cc_final: 0.7173 (t0) REVERT: B 707 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6263 (pp) REVERT: B 862 GLU cc_start: 0.7142 (pm20) cc_final: 0.6670 (pm20) REVERT: B 902 MET cc_start: 0.7981 (mmt) cc_final: 0.7660 (mmt) REVERT: C 141 MET cc_start: 0.8281 (mmt) cc_final: 0.7966 (mmt) outliers start: 41 outliers final: 30 residues processed: 299 average time/residue: 0.3420 time to fit residues: 162.3555 Evaluate side-chains 282 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 784 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 135 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 211 GLN B 729 ASN C 108 GLN C 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24642 Z= 0.231 Angle : 0.536 6.974 33248 Z= 0.278 Chirality : 0.042 0.167 3862 Planarity : 0.004 0.063 4158 Dihedral : 13.422 160.895 3940 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.16 % Allowed : 10.12 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 (0.15), residues: 3114 helix: 2.14 (0.13), residues: 1666 sheet: 0.62 (0.27), residues: 409 loop : -1.43 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 892 HIS 0.002 0.001 HIS A 688 PHE 0.013 0.001 PHE C1015 TYR 0.016 0.001 TYR A 755 ARG 0.007 0.001 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 259 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: B 135 ASN cc_start: 0.7545 (m-40) cc_final: 0.7217 (t0) REVERT: B 862 GLU cc_start: 0.7158 (pm20) cc_final: 0.6626 (pm20) REVERT: B 902 MET cc_start: 0.8046 (mmt) cc_final: 0.7799 (mmt) REVERT: C 78 MET cc_start: 0.8684 (mtm) cc_final: 0.8475 (mtm) REVERT: C 141 MET cc_start: 0.8242 (mmt) cc_final: 0.8013 (mmt) outliers start: 54 outliers final: 33 residues processed: 302 average time/residue: 0.3674 time to fit residues: 178.2796 Evaluate side-chains 283 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 784 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 269 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN B 729 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24642 Z= 0.231 Angle : 0.531 7.116 33248 Z= 0.276 Chirality : 0.042 0.160 3862 Planarity : 0.004 0.063 4158 Dihedral : 12.843 165.104 3940 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.12 % Allowed : 11.36 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.23 (0.15), residues: 3114 helix: 2.13 (0.13), residues: 1666 sheet: 0.67 (0.27), residues: 409 loop : -1.39 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1016 HIS 0.002 0.001 HIS A 688 PHE 0.014 0.001 PHE B 11 TYR 0.016 0.001 TYR A 49 ARG 0.007 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 2.506 Fit side-chains revert: symmetry clash REVERT: B 135 ASN cc_start: 0.7572 (m-40) cc_final: 0.7260 (t0) REVERT: B 707 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6218 (pp) REVERT: B 862 GLU cc_start: 0.7147 (pm20) cc_final: 0.6844 (pm20) REVERT: C 67 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7419 (mtm-85) REVERT: C 141 MET cc_start: 0.8212 (mmt) cc_final: 0.7977 (mmt) outliers start: 53 outliers final: 41 residues processed: 296 average time/residue: 0.3377 time to fit residues: 160.2292 Evaluate side-chains 291 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 249 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 823 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 300 optimal weight: 0.9980 chunk 249 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24642 Z= 0.167 Angle : 0.493 7.009 33248 Z= 0.256 Chirality : 0.040 0.146 3862 Planarity : 0.004 0.062 4158 Dihedral : 12.102 173.895 3940 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 11.80 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.44 (0.16), residues: 3114 helix: 2.30 (0.13), residues: 1661 sheet: 0.81 (0.27), residues: 407 loop : -1.28 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1016 HIS 0.002 0.000 HIS A 688 PHE 0.013 0.001 PHE C1015 TYR 0.013 0.001 TYR C 49 ARG 0.007 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 261 time to evaluate : 2.358 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: A 220 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.5908 (tp) REVERT: A 482 LEU cc_start: 0.8468 (tp) cc_final: 0.8232 (tp) REVERT: B 135 ASN cc_start: 0.7530 (m-40) cc_final: 0.7255 (t0) REVERT: B 843 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7403 (pttm) REVERT: B 862 GLU cc_start: 0.7135 (pm20) cc_final: 0.6462 (pm20) REVERT: C 67 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7453 (mtm-85) outliers start: 51 outliers final: 34 residues processed: 300 average time/residue: 0.3462 time to fit residues: 165.5557 Evaluate side-chains 286 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 799 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 0.0570 chunk 33 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN C 736 GLN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24642 Z= 0.207 Angle : 0.515 8.227 33248 Z= 0.266 Chirality : 0.041 0.292 3862 Planarity : 0.004 0.066 4158 Dihedral : 11.732 176.952 3940 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.36 % Allowed : 11.72 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.44 (0.15), residues: 3114 helix: 2.26 (0.13), residues: 1666 sheet: 0.84 (0.27), residues: 407 loop : -1.25 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1016 HIS 0.002 0.001 HIS A 688 PHE 0.014 0.001 PHE C 551 TYR 0.013 0.001 TYR C 49 ARG 0.007 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 253 time to evaluate : 2.586 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: A 220 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5997 (tp) REVERT: A 482 LEU cc_start: 0.8506 (tp) cc_final: 0.8285 (tp) REVERT: B 135 ASN cc_start: 0.7573 (m-40) cc_final: 0.7288 (t0) REVERT: B 843 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7438 (pttm) REVERT: B 862 GLU cc_start: 0.7144 (pm20) cc_final: 0.6478 (pm20) REVERT: C 141 MET cc_start: 0.8520 (mmt) cc_final: 0.8041 (mmt) outliers start: 59 outliers final: 50 residues processed: 299 average time/residue: 0.3461 time to fit residues: 165.3781 Evaluate side-chains 300 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 248 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 823 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 179 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 204 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN C 736 GLN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24642 Z= 0.157 Angle : 0.487 7.057 33248 Z= 0.252 Chirality : 0.040 0.280 3862 Planarity : 0.004 0.063 4158 Dihedral : 11.158 165.016 3940 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.28 % Allowed : 11.76 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.60 (0.16), residues: 3114 helix: 2.37 (0.13), residues: 1663 sheet: 0.98 (0.27), residues: 405 loop : -1.14 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1016 HIS 0.001 0.000 HIS C 688 PHE 0.012 0.001 PHE C 551 TYR 0.019 0.001 TYR A 362 ARG 0.008 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 252 time to evaluate : 2.909 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: A 220 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5772 (tp) REVERT: A 360 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6611 (mm) REVERT: A 482 LEU cc_start: 0.8439 (tp) cc_final: 0.8234 (tp) REVERT: B 135 ASN cc_start: 0.7549 (m-40) cc_final: 0.7317 (t0) REVERT: B 346 MET cc_start: 0.7690 (tpp) cc_final: 0.7455 (mmm) REVERT: B 843 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7386 (pttm) REVERT: B 862 GLU cc_start: 0.7127 (pm20) cc_final: 0.6812 (pm20) outliers start: 57 outliers final: 46 residues processed: 296 average time/residue: 0.3385 time to fit residues: 161.2832 Evaluate side-chains 294 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 245 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 823 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.318 > 50: distance: 1 - 15: 32.785 distance: 5 - 22: 30.663 distance: 9 - 33: 34.365 distance: 13 - 15: 34.673 distance: 14 - 41: 37.624 distance: 16 - 17: 40.169 distance: 17 - 18: 63.341 distance: 17 - 22: 40.144 distance: 18 - 52: 47.900 distance: 22 - 23: 29.865 distance: 23 - 24: 39.734 distance: 24 - 25: 40.313 distance: 24 - 33: 40.190 distance: 25 - 60: 13.616 distance: 26 - 27: 37.988 distance: 27 - 28: 20.791 distance: 27 - 29: 39.941 distance: 28 - 30: 24.734 distance: 29 - 31: 40.684 distance: 30 - 32: 20.923 distance: 31 - 32: 3.127 distance: 34 - 37: 40.308 distance: 35 - 41: 40.256 distance: 38 - 39: 50.399 distance: 41 - 42: 39.303 distance: 42 - 43: 40.172 distance: 42 - 45: 40.109 distance: 43 - 44: 17.007 distance: 43 - 52: 56.522 distance: 45 - 46: 39.020 distance: 46 - 48: 22.454 distance: 47 - 49: 40.476 distance: 48 - 50: 19.343 distance: 49 - 51: 39.448 distance: 50 - 51: 39.777 distance: 52 - 53: 8.314 distance: 53 - 54: 31.969 distance: 53 - 56: 10.318 distance: 54 - 55: 40.247 distance: 54 - 60: 10.174 distance: 56 - 57: 40.626 distance: 57 - 58: 39.346 distance: 58 - 59: 35.982 distance: 60 - 61: 10.334 distance: 61 - 62: 39.585 distance: 61 - 64: 38.859 distance: 62 - 63: 40.465 distance: 62 - 71: 45.192 distance: 65 - 66: 57.022 distance: 68 - 69: 40.996 distance: 68 - 70: 39.210 distance: 71 - 72: 60.821 distance: 72 - 73: 24.989 distance: 73 - 74: 14.772 distance: 73 - 79: 16.565 distance: 75 - 76: 8.763 distance: 76 - 77: 7.686 distance: 76 - 78: 52.479 distance: 79 - 85: 56.029 distance: 80 - 81: 40.474 distance: 80 - 83: 56.844 distance: 81 - 82: 40.116 distance: 87 - 88: 40.311 distance: 88 - 89: 39.932 distance: 90 - 92: 40.468 distance: 95 - 99: 35.533