Starting phenix.real_space_refine on Tue Nov 19 03:41:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b67_44248/11_2024/9b67_44248.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b67_44248/11_2024/9b67_44248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b67_44248/11_2024/9b67_44248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b67_44248/11_2024/9b67_44248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b67_44248/11_2024/9b67_44248.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b67_44248/11_2024/9b67_44248.cif" } resolution = 3.39 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= 0.004 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 11993 2.51 5 N 2968 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18435 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3136 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 404, 3136 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3186 Chain: "B" Number of atoms: 3152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3141 Classifications: {'peptide': 405} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 405, 3141 Classifications: {'peptide': 405} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3197 Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3129 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3139 Classifications: {'peptide': 405} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 405, 3139 Classifications: {'peptide': 405} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3190 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.85 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.15 residue: pdb=" N APHE B 623 " occ=0.67 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.33 residue: pdb=" N APHE D 623 " occ=0.75 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.25 Time building chain proxies: 15.13, per 1000 atoms: 0.82 Number of scatterers: 18435 At special positions: 0 Unit cell: (115.62, 108.24, 146.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3346 8.00 N 2968 7.00 C 11993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 3.5 seconds 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 23 sheets defined 61.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 84 through 88 removed outlier: 4.391A pdb=" N ALA H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 105 Processing helix chain 'H' and resid 105 through 126 removed outlier: 4.047A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.692A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.566A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.982A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.686A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.693A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.725A pdb=" N GLY C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.722A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.613A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 547 through 551' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.552A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.915A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.838A pdb=" N MET C 670 " --> pdb=" O VAL C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.759A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.572A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.926A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.515A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.865A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.902A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.525A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 822 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.852A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.551A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.924A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.682A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.511A pdb=" N ALA A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 825 removed outlier: 4.048A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.944A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.585A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.835A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.746A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.793A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.526A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.554A pdb=" N ALA D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 822 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.800A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.584A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 127 removed outlier: 3.855A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.892A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.527A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.672A pdb=" N VAL F 57 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 removed outlier: 5.981A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.751A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.324A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.612A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 479 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.612A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 479 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.766A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.331A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.512A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA A 477 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.512A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA A 477 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.452A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.300A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU D 479 " --> pdb=" O ASP D 733 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.300A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU D 479 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.582A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.339A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC5, first strand: chain 'G' and resid 34 through 38 removed outlier: 3.520A pdb=" N HIS G 60 " --> pdb=" O CYS G 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS G 67 " --> pdb=" O HIS G 60 " (cutoff:3.500A) 1175 hydrogen bonds defined for protein. 3415 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: 6.51 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5709 1.36 - 1.49: 5174 1.49 - 1.62: 7759 1.62 - 1.75: 2 1.75 - 1.89: 207 Bond restraints: 18851 Sorted by residual: bond pdb=" N PRO C 632 " pdb=" CD PRO C 632 " ideal model delta sigma weight residual 1.473 1.422 0.051 1.40e-02 5.10e+03 1.35e+01 bond pdb=" CB PRO C 632 " pdb=" CG PRO C 632 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.94e+00 bond pdb=" CB CYS H 77 " pdb=" SG CYS H 77 " ideal model delta sigma weight residual 1.808 1.888 -0.080 3.30e-02 9.18e+02 5.80e+00 bond pdb=" CB CYS H 67 " pdb=" SG CYS H 67 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.19e+00 bond pdb=" CA PRO C 632 " pdb=" CB PRO C 632 " ideal model delta sigma weight residual 1.531 1.554 -0.023 1.49e-02 4.50e+03 2.47e+00 ... (remaining 18846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 25400 2.80 - 5.61: 81 5.61 - 8.41: 10 8.41 - 11.22: 1 11.22 - 14.02: 1 Bond angle restraints: 25493 Sorted by residual: angle pdb=" CA PRO C 632 " pdb=" N PRO C 632 " pdb=" CD PRO C 632 " ideal model delta sigma weight residual 112.00 97.98 14.02 1.40e+00 5.10e-01 1.00e+02 angle pdb=" CB MET D 408 " pdb=" CG MET D 408 " pdb=" SD MET D 408 " ideal model delta sigma weight residual 112.70 122.35 -9.65 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA CYS H 67 " pdb=" CB CYS H 67 " pdb=" SG CYS H 67 " ideal model delta sigma weight residual 114.40 121.69 -7.29 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CB LYS A 699 " pdb=" CG LYS A 699 " pdb=" CD LYS A 699 " ideal model delta sigma weight residual 111.30 118.52 -7.22 2.30e+00 1.89e-01 9.86e+00 angle pdb=" C CYS H 67 " pdb=" CA CYS H 67 " pdb=" CB CYS H 67 " ideal model delta sigma weight residual 109.94 115.40 -5.46 2.13e+00 2.20e-01 6.58e+00 ... (remaining 25488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 9471 18.04 - 36.09: 1176 36.09 - 54.13: 314 54.13 - 72.17: 40 72.17 - 90.21: 22 Dihedral angle restraints: 11023 sinusoidal: 4201 harmonic: 6822 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual -86.00 -176.21 90.21 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -166.01 80.01 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual -86.00 -31.09 -54.91 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 11020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2063 0.037 - 0.074: 639 0.074 - 0.112: 140 0.112 - 0.149: 27 0.149 - 0.186: 2 Chirality restraints: 2871 Sorted by residual: chirality pdb=" CG LEU H 76 " pdb=" CB LEU H 76 " pdb=" CD1 LEU H 76 " pdb=" CD2 LEU H 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CB ILE H 80 " pdb=" CA ILE H 80 " pdb=" CG1 ILE H 80 " pdb=" CG2 ILE H 80 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CG LEU F 23 " pdb=" CB LEU F 23 " pdb=" CD1 LEU F 23 " pdb=" CD2 LEU F 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2868 not shown) Planarity restraints: 3147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 631 " 0.087 5.00e-02 4.00e+02 1.21e-01 2.36e+01 pdb=" N PRO C 632 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO C 632 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 632 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 744 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO D 745 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 745 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 745 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO C 717 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " 0.024 5.00e-02 4.00e+02 ... (remaining 3144 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 525 2.71 - 3.26: 18448 3.26 - 3.81: 31208 3.81 - 4.35: 37339 4.35 - 4.90: 64072 Nonbonded interactions: 151592 Sorted by model distance: nonbonded pdb=" OH TYR H 174 " pdb=" OE2 GLU D 524 " model vdw 2.168 3.040 nonbonded pdb=" OD2 ASP D 454 " pdb=" OG1 THR D 457 " model vdw 2.175 3.040 nonbonded pdb=" OD2 ASP B 454 " pdb=" OG1 THR B 457 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR D 685 " pdb=" OE1 GLU D 688 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.227 3.040 ... (remaining 151587 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 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 6 \ 60 or (resid 661 and (name N or name CA or name C or name O or name CB )) or res \ id 662 through 763 or resid 765 through 812 or (resid 813 and (name N or name CA \ or name C or name O or name CB )) or resid 814 through 818 or (resid 819 throug \ h 820 and (name N or name CA or name C or name O or name CB )) or resid 821 thro \ ugh 822)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 506 or (resid 511 and (name N or name CA or name C or name \ O or name CB )) or resid 512 through 575 or (resid 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 through 593 or (resid 594 and (nam \ e N or name CA or name C or name O or name CB )) or resid 595 through 622 or res \ id 624 through 626 or (resid 627 and (name N or name CA or name C or name O or n \ ame CB )) or resid 628 through 763 or resid 765 through 773 or (resid 784 and (n \ ame N or name CA or name C or name O or name CB )) or resid 785 through 822)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 660 or (resid 661 and (name N or name CA or \ name C or name O or name CB )) or resid 662 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 763 or resid \ 765 through 812 or (resid 813 and (name N or name CA or name C or name O or nam \ e CB )) or resid 814 through 818 or (resid 819 through 820 and (name N or name C \ A or name C or name O or name CB )) or resid 821 through 822)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 506 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 763 or resid \ 765 through 773 or (resid 784 and (name N or name CA or name C or name O or nam \ e CB )) or resid 785 through 822)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214)) } 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=0.15 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 47.630 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 18851 Z= 0.221 Angle : 0.483 14.020 25493 Z= 0.257 Chirality : 0.038 0.186 2871 Planarity : 0.004 0.121 3147 Dihedral : 16.881 86.785 6633 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.26 % Allowed : 23.58 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.18), residues: 2331 helix: 2.43 (0.14), residues: 1349 sheet: -1.17 (0.36), residues: 200 loop : -0.49 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 551 HIS 0.004 0.001 HIS E 60 PHE 0.013 0.001 PHE A 659 TYR 0.018 0.001 TYR C 647 ARG 0.003 0.000 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 276 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 425 CYS cc_start: 0.8605 (m) cc_final: 0.8372 (m) REVERT: A 551 TRP cc_start: 0.4586 (m100) cc_final: 0.4189 (m100) outliers start: 5 outliers final: 2 residues processed: 279 average time/residue: 0.3280 time to fit residues: 137.5613 Evaluate side-chains 268 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain C residue 542 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 0.0970 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18851 Z= 0.138 Angle : 0.438 7.924 25493 Z= 0.236 Chirality : 0.038 0.124 2871 Planarity : 0.003 0.061 3147 Dihedral : 3.317 39.090 2559 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.80 % Allowed : 21.88 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.18), residues: 2331 helix: 3.02 (0.13), residues: 1375 sheet: -1.13 (0.35), residues: 200 loop : -0.42 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 766 HIS 0.005 0.001 HIS E 60 PHE 0.012 0.001 PHE H 142 TYR 0.008 0.001 TYR C 702 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 2.012 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2051 (OUTLIER) cc_final: 0.1726 (p0) REVERT: B 637 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: A 463 MET cc_start: 0.8226 (mtm) cc_final: 0.7900 (mtm) REVERT: A 467 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7974 (mm) REVERT: A 551 TRP cc_start: 0.4172 (m100) cc_final: 0.3576 (m100) REVERT: E 97 PHE cc_start: 0.7211 (t80) cc_final: 0.6915 (t80) REVERT: E 149 ASN cc_start: 0.8811 (t0) cc_final: 0.8474 (t0) outliers start: 35 outliers final: 17 residues processed: 329 average time/residue: 0.3068 time to fit residues: 153.8413 Evaluate side-chains 298 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain G residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 209 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18851 Z= 0.240 Angle : 0.492 9.587 25493 Z= 0.259 Chirality : 0.039 0.137 2871 Planarity : 0.004 0.057 3147 Dihedral : 3.402 15.144 2555 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.88 % Allowed : 21.42 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.18), residues: 2331 helix: 2.83 (0.13), residues: 1375 sheet: -1.10 (0.35), residues: 200 loop : -0.48 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 766 HIS 0.005 0.001 HIS E 205 PHE 0.014 0.002 PHE F 201 TYR 0.015 0.001 TYR F 96 ARG 0.006 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2119 (OUTLIER) cc_final: 0.1780 (p0) REVERT: C 425 CYS cc_start: 0.8593 (m) cc_final: 0.8336 (m) REVERT: B 637 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: B 703 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8209 (mp) REVERT: A 421 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: A 463 MET cc_start: 0.8297 (mtm) cc_final: 0.7980 (mtm) REVERT: A 467 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8005 (mm) REVERT: A 551 TRP cc_start: 0.4516 (m100) cc_final: 0.3759 (m100) REVERT: G 67 CYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6433 (m) REVERT: G 149 ASN cc_start: 0.8852 (t0) cc_final: 0.8597 (t0) outliers start: 56 outliers final: 28 residues processed: 332 average time/residue: 0.3208 time to fit residues: 161.8541 Evaluate side-chains 308 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS C 747 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN D 756 GLN E 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18851 Z= 0.224 Angle : 0.477 9.734 25493 Z= 0.252 Chirality : 0.039 0.131 2871 Planarity : 0.004 0.055 3147 Dihedral : 3.429 15.514 2555 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.09 % Allowed : 21.52 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.18), residues: 2331 helix: 2.82 (0.13), residues: 1375 sheet: -1.15 (0.35), residues: 200 loop : -0.51 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 766 HIS 0.005 0.001 HIS E 205 PHE 0.012 0.001 PHE F 201 TYR 0.012 0.001 TYR B 711 ARG 0.007 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 291 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2134 (OUTLIER) cc_final: 0.1785 (p0) REVERT: H 117 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7505 (mpp) REVERT: C 425 CYS cc_start: 0.8621 (m) cc_final: 0.8414 (m) REVERT: B 405 TYR cc_start: 0.8401 (m-80) cc_final: 0.8152 (m-80) REVERT: B 637 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: B 703 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 463 MET cc_start: 0.8282 (mtm) cc_final: 0.7913 (mtm) REVERT: A 467 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8018 (mm) REVERT: D 486 GLU cc_start: 0.7201 (tp30) cc_final: 0.6849 (tp30) REVERT: E 65 ARG cc_start: 0.7370 (ptm160) cc_final: 0.6668 (ptm160) REVERT: E 85 GLU cc_start: 0.3025 (OUTLIER) cc_final: 0.2707 (mp0) outliers start: 60 outliers final: 37 residues processed: 332 average time/residue: 0.3106 time to fit residues: 157.5819 Evaluate side-chains 321 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 201 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS C 747 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN E 160 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18851 Z= 0.229 Angle : 0.487 10.791 25493 Z= 0.256 Chirality : 0.039 0.133 2871 Planarity : 0.004 0.060 3147 Dihedral : 3.466 15.593 2555 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.09 % Allowed : 22.14 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.18), residues: 2331 helix: 2.78 (0.14), residues: 1375 sheet: -1.08 (0.38), residues: 172 loop : -0.58 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 766 HIS 0.005 0.001 HIS E 205 PHE 0.012 0.001 PHE F 201 TYR 0.013 0.001 TYR B 711 ARG 0.006 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 292 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2057 (OUTLIER) cc_final: 0.1684 (p0) REVERT: H 117 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7499 (mpp) REVERT: C 425 CYS cc_start: 0.8607 (m) cc_final: 0.8402 (m) REVERT: B 405 TYR cc_start: 0.8402 (m-80) cc_final: 0.7679 (m-80) REVERT: B 637 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: B 703 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8218 (mp) REVERT: A 467 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8045 (mm) REVERT: D 486 GLU cc_start: 0.7145 (tp30) cc_final: 0.6761 (tp30) REVERT: E 65 ARG cc_start: 0.7389 (ptm160) cc_final: 0.6701 (ptm160) REVERT: E 85 GLU cc_start: 0.3044 (OUTLIER) cc_final: 0.2705 (mp0) REVERT: G 149 ASN cc_start: 0.8839 (t0) cc_final: 0.8610 (t0) outliers start: 60 outliers final: 39 residues processed: 332 average time/residue: 0.3138 time to fit residues: 159.8161 Evaluate side-chains 324 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: