Starting phenix.real_space_refine on Wed Jan 22 10:09:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b67_44248/01_2025/9b67_44248.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b67_44248/01_2025/9b67_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/cci-nas-00/data/ceres_data/9b67_44248/01_2025/9b67_44248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b67_44248/01_2025/9b67_44248.map" model { file = "/net/cci-nas-00/data/ceres_data/9b67_44248/01_2025/9b67_44248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b67_44248/01_2025/9b67_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-5571/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: 15.27, per 1000 atoms: 0.83 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: 4.28 Conformation dependent library (CDL) restraints added in 3.4 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: 2.79 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: 6.88 Time building geometry restraints manager: 5.08 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: 2.390 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: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.050 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 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:2.750 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.220 ------------------------------------------------------------------------------- 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 : 1.893 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: 0.3260 time to fit residues: 136.8316 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 : 2.040 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.159974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.125748 restraints weight = 57131.480| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.32 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 2.009 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1970 (OUTLIER) cc_final: 0.1616 (p0) REVERT: B 637 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6491 (pm20) REVERT: A 463 MET cc_start: 0.7923 (mtm) cc_final: 0.7695 (mtm) REVERT: A 467 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7935 (mm) REVERT: A 551 TRP cc_start: 0.4044 (m100) cc_final: 0.3423 (m100) REVERT: E 97 PHE cc_start: 0.7045 (t80) cc_final: 0.6762 (t80) REVERT: E 149 ASN cc_start: 0.8662 (t0) cc_final: 0.8336 (t0) outliers start: 35 outliers final: 17 residues processed: 329 average time/residue: 0.3314 time to fit residues: 167.4198 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 : 2.110 ------------------------------------------------------------------------------- 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 180 optimal weight: 0.4980 chunk 172 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.161249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135978 restraints weight = 52636.152| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.49 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18851 Z= 0.131 Angle : 0.428 10.222 25493 Z= 0.225 Chirality : 0.037 0.122 2871 Planarity : 0.003 0.058 3147 Dihedral : 3.113 15.593 2555 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.11 % Allowed : 21.88 % Favored : 76.00 % 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: 2.52 (0.18), residues: 2331 helix: 3.12 (0.13), residues: 1389 sheet: -1.03 (0.35), residues: 200 loop : -0.44 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 766 HIS 0.004 0.001 HIS E 60 PHE 0.013 0.001 PHE H 142 TYR 0.017 0.001 TYR F 96 ARG 0.005 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 343 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 1.872 Fit side-chains revert: symmetry clash REVERT: H 65 ARG cc_start: 0.6079 (ptt90) cc_final: 0.5312 (ptp-170) REVERT: H 86 ASP cc_start: 0.2053 (OUTLIER) cc_final: 0.1714 (p0) REVERT: C 425 CYS cc_start: 0.7710 (m) cc_final: 0.7384 (m) REVERT: C 720 THR cc_start: 0.7935 (p) cc_final: 0.7573 (p) REVERT: B 637 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6597 (pm20) REVERT: B 703 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 467 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 551 TRP cc_start: 0.4017 (m100) cc_final: 0.3542 (m100) REVERT: D 486 GLU cc_start: 0.6737 (tp30) cc_final: 0.6471 (tp30) REVERT: E 149 ASN cc_start: 0.8526 (t0) cc_final: 0.8155 (t0) REVERT: G 149 ASN cc_start: 0.8410 (t0) cc_final: 0.8173 (t0) outliers start: 41 outliers final: 20 residues processed: 326 average time/residue: 0.3339 time to fit residues: 164.5182 Evaluate side-chains 304 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 443 THR Chi-restraints excluded: chain C residue 681 VAL 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 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 729 SER Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 744 THR 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 179 SER Chi-restraints excluded: chain G residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 158 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 217 optimal weight: 0.6980 chunk 211 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.150429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.115700 restraints weight = 55962.231| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.16 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 18851 Z= 0.434 Angle : 0.613 12.866 25493 Z= 0.324 Chirality : 0.044 0.159 2871 Planarity : 0.005 0.055 3147 Dihedral : 3.887 15.166 2555 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.76 % Allowed : 21.16 % Favored : 75.08 % 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: 1.59 (0.17), residues: 2331 helix: 2.31 (0.14), residues: 1371 sheet: -1.17 (0.35), residues: 198 loop : -0.65 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 551 HIS 0.008 0.002 HIS F 60 PHE 0.018 0.002 PHE D 571 TYR 0.018 0.002 TYR B 816 ARG 0.009 0.001 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 362 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 289 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ASP cc_start: 0.7021 (m-30) cc_final: 0.6706 (m-30) REVERT: H 86 ASP cc_start: 0.2009 (OUTLIER) cc_final: 0.1627 (p0) REVERT: H 117 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7514 (mpp) REVERT: C 425 CYS cc_start: 0.8051 (m) cc_final: 0.7847 (m) REVERT: B 703 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 467 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8001 (mm) REVERT: E 65 ARG cc_start: 0.7269 (ptm160) cc_final: 0.6693 (ptm160) REVERT: E 85 GLU cc_start: 0.3201 (OUTLIER) cc_final: 0.2882 (mp0) outliers start: 73 outliers final: 43 residues processed: 337 average time/residue: 0.3287 time to fit residues: 169.7261 Evaluate side-chains 323 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 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 546 PHE Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 721 MET 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 746 VAL 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 11 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 80 ILE 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 208 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 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 18 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 86 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN E 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.156870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122858 restraints weight = 54489.010| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.19 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1575 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= 0.136 Angle : 0.445 9.604 25493 Z= 0.235 Chirality : 0.038 0.124 2871 Planarity : 0.003 0.052 3147 Dihedral : 3.389 16.754 2555 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.27 % Allowed : 23.07 % Favored : 74.67 % 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: 2.28 (0.18), residues: 2331 helix: 2.93 (0.14), residues: 1375 sheet: -1.11 (0.36), residues: 188 loop : -0.48 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 766 HIS 0.005 0.001 HIS E 205 PHE 0.013 0.001 PHE H 116 TYR 0.013 0.001 TYR B 711 ARG 0.005 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 345 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 301 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1930 (OUTLIER) cc_final: 0.1512 (p0) REVERT: H 117 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7402 (mpp) REVERT: C 425 CYS cc_start: 0.7998 (m) cc_final: 0.7779 (m) REVERT: B 637 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6449 (pm20) REVERT: B 703 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 463 MET cc_start: 0.7730 (mtm) cc_final: 0.7360 (mtm) REVERT: A 467 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8001 (mm) REVERT: E 65 ARG cc_start: 0.7231 (ptm160) cc_final: 0.6767 (ptm160) REVERT: G 149 ASN cc_start: 0.8680 (t0) cc_final: 0.8375 (t0) outliers start: 44 outliers final: 26 residues processed: 331 average time/residue: 0.3129 time to fit residues: 158.3277 Evaluate side-chains 314 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 464 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU 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 713 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 592 SER 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 E residue 134 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 128 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 189 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN E 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.156759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131563 restraints weight = 52359.688| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.39 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18851 Z= 0.196 Angle : 0.470 11.382 25493 Z= 0.247 Chirality : 0.038 0.130 2871 Planarity : 0.004 0.062 3147 Dihedral : 3.396 16.248 2555 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.52 % Allowed : 22.55 % Favored : 74.92 % 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: 2.19 (0.18), residues: 2331 helix: 2.87 (0.14), residues: 1375 sheet: -1.17 (0.38), residues: 172 loop : -0.56 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 551 HIS 0.005 0.001 HIS E 205 PHE 0.015 0.001 PHE A 659 TYR 0.014 0.001 TYR B 711 ARG 0.008 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 6 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 343 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1918 (OUTLIER) cc_final: 0.1531 (p0) REVERT: H 117 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7371 (mpp) REVERT: C 422 GLU cc_start: 0.6393 (tt0) cc_final: 0.5807 (tt0) REVERT: C 425 CYS cc_start: 0.7992 (m) cc_final: 0.7753 (m) REVERT: B 416 GLU cc_start: 0.4950 (tp30) cc_final: 0.4437 (tt0) REVERT: B 637 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: B 703 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 467 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7914 (mm) REVERT: E 65 ARG cc_start: 0.7366 (ptm160) cc_final: 0.6815 (ptm160) REVERT: E 149 ASN cc_start: 0.8425 (t0) cc_final: 0.8144 (t0) REVERT: G 67 CYS cc_start: 0.6366 (OUTLIER) cc_final: 0.6139 (m) REVERT: G 149 ASN cc_start: 0.8569 (t0) cc_final: 0.8205 (t0) outliers start: 49 outliers final: 31 residues processed: 326 average time/residue: 0.3156 time to fit residues: 156.8926 Evaluate side-chains 317 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 484 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU 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 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 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 128 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 225 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.156685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131442 restraints weight = 54161.730| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 4.69 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18851 Z= 0.144 Angle : 0.437 10.315 25493 Z= 0.230 Chirality : 0.037 0.127 2871 Planarity : 0.003 0.056 3147 Dihedral : 3.260 15.902 2555 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.16 % Allowed : 23.22 % Favored : 74.61 % 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: 2.39 (0.18), residues: 2331 helix: 3.05 (0.14), residues: 1377 sheet: -1.12 (0.38), residues: 172 loop : -0.53 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 766 HIS 0.007 0.001 HIS E 205 PHE 0.014 0.001 PHE A 659 TYR 0.012 0.001 TYR A 549 ARG 0.007 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 7 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 339 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 ARG cc_start: 0.6244 (ptt90) cc_final: 0.5475 (ptp-170) REVERT: H 86 ASP cc_start: 0.2167 (OUTLIER) cc_final: 0.1758 (p0) REVERT: H 117 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7426 (mpp) REVERT: H 131 ARG cc_start: 0.5100 (tpt-90) cc_final: 0.3862 (mtp180) REVERT: C 422 GLU cc_start: 0.6427 (tt0) cc_final: 0.5952 (tt0) REVERT: C 425 CYS cc_start: 0.7818 (m) cc_final: 0.7585 (m) REVERT: C 756 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7084 (mt0) REVERT: B 416 GLU cc_start: 0.4883 (tp30) cc_final: 0.4407 (tt0) REVERT: B 637 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: B 703 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 467 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7997 (mm) REVERT: A 545 ARG cc_start: 0.7821 (mmt90) cc_final: 0.7395 (mmt90) REVERT: E 65 ARG cc_start: 0.7332 (ptm160) cc_final: 0.6812 (ptm160) REVERT: E 149 ASN cc_start: 0.8289 (t0) cc_final: 0.7945 (t0) REVERT: G 149 ASN cc_start: 0.8454 (t0) cc_final: 0.8022 (t0) outliers start: 42 outliers final: 29 residues processed: 325 average time/residue: 0.3111 time to fit residues: 153.5425 Evaluate side-chains 319 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 67 CYS 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 443 THR Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU 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 746 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 407 MET 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 134 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.155918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121929 restraints weight = 58063.046| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.40 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18851 Z= 0.205 Angle : 0.477 10.620 25493 Z= 0.248 Chirality : 0.039 0.130 2871 Planarity : 0.004 0.061 3147 Dihedral : 3.361 16.223 2555 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.32 % Allowed : 23.07 % Favored : 74.61 % 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: 2.20 (0.18), residues: 2331 helix: 2.89 (0.13), residues: 1375 sheet: -1.20 (0.38), residues: 172 loop : -0.57 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 551 HIS 0.008 0.001 HIS E 205 PHE 0.019 0.001 PHE A 659 TYR 0.013 0.001 TYR B 711 ARG 0.004 0.000 ARG B 675 *********************** REFINEMENT MACRO_CYCLE 8 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 332 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2350 (OUTLIER) cc_final: 0.1901 (p0) REVERT: H 117 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7429 (mpp) REVERT: C 422 GLU cc_start: 0.6280 (tt0) cc_final: 0.5701 (tt0) REVERT: C 425 CYS cc_start: 0.7953 (m) cc_final: 0.7747 (m) REVERT: B 416 GLU cc_start: 0.4698 (tp30) cc_final: 0.4323 (tt0) REVERT: B 637 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6491 (pm20) REVERT: B 703 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 467 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8006 (mm) REVERT: E 65 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6786 (ptm160) REVERT: E 149 ASN cc_start: 0.8589 (t0) cc_final: 0.8284 (t0) outliers start: 45 outliers final: 32 residues processed: 315 average time/residue: 0.3218 time to fit residues: 154.2412 Evaluate side-chains 321 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 67 CYS 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 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU 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 746 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 488 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 8 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 13 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 209 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.155592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130235 restraints weight = 52009.151| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.48 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18851 Z= 0.196 Angle : 0.472 10.294 25493 Z= 0.246 Chirality : 0.039 0.129 2871 Planarity : 0.004 0.058 3147 Dihedral : 3.378 16.381 2555 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.16 % Allowed : 23.33 % Favored : 74.51 % 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: 2.19 (0.18), residues: 2331 helix: 2.87 (0.13), residues: 1375 sheet: -1.10 (0.38), residues: 168 loop : -0.60 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 551 HIS 0.008 0.001 HIS E 205 PHE 0.016 0.001 PHE H 116 TYR 0.012 0.001 TYR B 711 ARG 0.009 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 9 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 326 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 ARG cc_start: 0.6017 (ptt90) cc_final: 0.5422 (ptp-170) REVERT: H 117 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7433 (mpp) REVERT: C 422 GLU cc_start: 0.6373 (tt0) cc_final: 0.5759 (tt0) REVERT: C 425 CYS cc_start: 0.7967 (m) cc_final: 0.7744 (m) REVERT: B 416 GLU cc_start: 0.4805 (tp30) cc_final: 0.4406 (tt0) REVERT: B 637 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6598 (pm20) REVERT: B 703 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 463 MET cc_start: 0.8077 (mtm) cc_final: 0.7706 (mtm) REVERT: A 467 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7918 (mm) REVERT: E 65 ARG cc_start: 0.7352 (ptm160) cc_final: 0.6833 (ptm160) outliers start: 42 outliers final: 34 residues processed: 312 average time/residue: 0.3167 time to fit residues: 150.0297 Evaluate side-chains 319 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 175 SER 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 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU 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 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 488 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 8 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 179 optimal weight: 0.0570 chunk 208 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.158075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124663 restraints weight = 59161.901| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.37 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18851 Z= 0.131 Angle : 0.449 13.065 25493 Z= 0.231 Chirality : 0.038 0.124 2871 Planarity : 0.003 0.056 3147 Dihedral : 3.216 17.008 2555 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.01 % Allowed : 23.58 % Favored : 74.41 % 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: 2.39 (0.18), residues: 2331 helix: 3.04 (0.14), residues: 1389 sheet: -1.05 (0.38), residues: 168 loop : -0.58 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 551 HIS 0.007 0.001 HIS E 205 PHE 0.017 0.001 PHE H 116 TYR 0.012 0.001 TYR B 711 ARG 0.007 0.000 ARG H 65 ********************** REFINEMENT MACRO_CYCLE 10 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 337 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 117 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7472 (mpp) REVERT: H 131 ARG cc_start: 0.5302 (tpt-90) cc_final: 0.4142 (mtp180) REVERT: C 422 GLU cc_start: 0.6285 (tt0) cc_final: 0.5836 (tt0) REVERT: B 416 GLU cc_start: 0.4557 (tp30) cc_final: 0.4251 (tt0) REVERT: B 637 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6541 (pm20) REVERT: B 703 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8067 (mp) REVERT: A 467 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7996 (mm) REVERT: E 65 ARG cc_start: 0.7300 (ptm160) cc_final: 0.6938 (ptm160) REVERT: E 149 ASN cc_start: 0.8573 (t0) cc_final: 0.8276 (t0) outliers start: 39 outliers final: 32 residues processed: 324 average time/residue: 0.3335 time to fit residues: 164.1953 Evaluate side-chains 318 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 67 CYS 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 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU 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 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 488 VAL Chi-restraints excluded: chain D residue 592 SER 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 8 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 86 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 216 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.160843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135862 restraints weight = 49769.623| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 4.36 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18851 Z= 0.136 Angle : 0.457 12.533 25493 Z= 0.235 Chirality : 0.038 0.132 2871 Planarity : 0.003 0.059 3147 Dihedral : 3.192 16.424 2555 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.96 % Allowed : 23.74 % Favored : 74.30 % 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: 2.40 (0.18), residues: 2331 helix: 3.03 (0.13), residues: 1389 sheet: -1.03 (0.38), residues: 168 loop : -0.57 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 551 HIS 0.007 0.001 HIS E 205 PHE 0.018 0.001 PHE H 116 TYR 0.011 0.001 TYR B 711 ARG 0.007 0.000 ARG H 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6681.96 seconds wall clock time: 124 minutes 30.70 seconds (7470.70 seconds total)