Starting phenix.real_space_refine on Sun Aug 24 08:22:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b67_44248/08_2025/9b67_44248.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b67_44248/08_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_44248/08_2025/9b67_44248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b67_44248/08_2025/9b67_44248.map" model { file = "/net/cci-nas-00/data/ceres_data/9b67_44248/08_2025/9b67_44248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b67_44248/08_2025/9b67_44248.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 1, 'ARG: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: {'ASP:plan': 1, 'ARG: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: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU: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: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU: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: {'ARG:plan': 2, 'PHE:plan': 1, '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: 5.74, per 1000 atoms: 0.31 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: 1.50 Conformation dependent library (CDL) restraints added in 971.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.80 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: 3.40 Time building geometry restraints manager: 1.90 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.930 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- 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 18863 Z= 0.139 Angle : 0.487 14.020 25517 Z= 0.259 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.18), 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 ARG 0.003 0.000 ARG D 694 TYR 0.018 0.001 TYR C 647 PHE 0.013 0.001 PHE A 659 TRP 0.020 0.001 TRP A 551 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00329 (18851) covalent geometry : angle 0.48282 (25493) SS BOND : bond 0.00381 ( 12) SS BOND : angle 2.17309 ( 24) hydrogen bonds : bond 0.19104 ( 1162) hydrogen bonds : angle 5.57091 ( 3415) *********************** 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 : 0.637 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: 0.1453 time to fit residues: 61.1838 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 : 0.705 ------------------------------------------------------------------------------- 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 216 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.157457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.131752 restraints weight = 49936.978| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.39 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18863 Z= 0.120 Angle : 0.458 7.913 25517 Z= 0.246 Chirality : 0.038 0.123 2871 Planarity : 0.003 0.061 3147 Dihedral : 3.398 39.299 2559 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.96 % Allowed : 22.19 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.18), residues: 2331 helix: 2.91 (0.13), residues: 1375 sheet: -1.14 (0.35), residues: 200 loop : -0.46 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 420 TYR 0.009 0.001 TYR C 440 PHE 0.011 0.001 PHE H 142 TRP 0.017 0.001 TRP A 766 HIS 0.005 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00263 (18851) covalent geometry : angle 0.45696 (25493) SS BOND : bond 0.00219 ( 12) SS BOND : angle 1.20304 ( 24) hydrogen bonds : bond 0.04294 ( 1162) hydrogen bonds : angle 3.86907 ( 3415) *********************** 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 341 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1918 (OUTLIER) cc_final: 0.1577 (p0) REVERT: F 31 ASP cc_start: 0.6974 (p0) cc_final: 0.6720 (p0) REVERT: C 425 CYS cc_start: 0.8030 (m) cc_final: 0.7691 (m) REVERT: B 637 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6587 (pm20) REVERT: B 703 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 463 MET cc_start: 0.7971 (mtm) cc_final: 0.7730 (mtm) REVERT: A 467 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7937 (mm) REVERT: A 551 TRP cc_start: 0.4179 (m100) cc_final: 0.3613 (m100) REVERT: A 569 ASN cc_start: 0.7538 (p0) cc_final: 0.7235 (p0) REVERT: E 97 PHE cc_start: 0.7022 (t80) cc_final: 0.6779 (t80) REVERT: E 149 ASN cc_start: 0.8496 (t0) cc_final: 0.8154 (t0) outliers start: 38 outliers final: 19 residues processed: 327 average time/residue: 0.1313 time to fit residues: 66.4062 Evaluate side-chains 298 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 ILE 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 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 729 SER Chi-restraints excluded: chain D residue 744 THR 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 140 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 66 optimal weight: 8.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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 D 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.153384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.117669 restraints weight = 64686.301| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.46 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18863 Z= 0.183 Angle : 0.518 10.395 25517 Z= 0.274 Chirality : 0.040 0.141 2871 Planarity : 0.004 0.057 3147 Dihedral : 3.580 15.509 2557 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.30 % Allowed : 21.32 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.18), residues: 2331 helix: 2.66 (0.13), residues: 1375 sheet: -1.20 (0.35), residues: 200 loop : -0.54 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 65 TYR 0.013 0.002 TYR C 700 PHE 0.016 0.002 PHE F 201 TRP 0.019 0.002 TRP D 766 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00434 (18851) covalent geometry : angle 0.51684 (25493) SS BOND : bond 0.00375 ( 12) SS BOND : angle 1.40885 ( 24) hydrogen bonds : bond 0.04625 ( 1162) hydrogen bonds : angle 3.93081 ( 3415) *********************** 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 349 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 285 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2070 (OUTLIER) cc_final: 0.1717 (p0) REVERT: H 117 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7486 (mpp) REVERT: C 425 CYS cc_start: 0.8073 (m) cc_final: 0.7853 (m) REVERT: B 637 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: B 703 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8122 (mp) REVERT: A 463 MET cc_start: 0.8066 (mtm) cc_final: 0.7777 (mtm) REVERT: A 467 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7999 (mm) REVERT: A 551 TRP cc_start: 0.4409 (m100) cc_final: 0.3719 (m100) REVERT: E 65 ARG cc_start: 0.7224 (ptm160) cc_final: 0.6586 (ptm160) outliers start: 64 outliers final: 31 residues processed: 330 average time/residue: 0.1262 time to fit residues: 64.2427 Evaluate side-chains 313 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 H residue 192 MET Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 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 744 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE 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 77 CYS Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 19 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.157384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123852 restraints weight = 59072.735| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.25 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18863 Z= 0.101 Angle : 0.433 10.515 25517 Z= 0.230 Chirality : 0.037 0.123 2871 Planarity : 0.003 0.054 3147 Dihedral : 3.278 15.827 2557 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.37 % Allowed : 22.19 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.18), residues: 2331 helix: 3.06 (0.14), residues: 1375 sheet: -1.18 (0.35), residues: 200 loop : -0.47 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.012 0.001 TYR B 711 PHE 0.012 0.001 PHE H 142 TRP 0.015 0.001 TRP D 766 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00217 (18851) covalent geometry : angle 0.43205 (25493) SS BOND : bond 0.00191 ( 12) SS BOND : angle 1.14590 ( 24) hydrogen bonds : bond 0.03654 ( 1162) hydrogen bonds : angle 3.55792 ( 3415) *********************** 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 347 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2128 (OUTLIER) cc_final: 0.1721 (p0) REVERT: C 425 CYS cc_start: 0.8109 (m) cc_final: 0.7882 (m) REVERT: B 637 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6445 (pm20) REVERT: B 673 TYR cc_start: 0.6386 (t80) cc_final: 0.6156 (t80) REVERT: A 396 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7775 (p) REVERT: A 463 MET cc_start: 0.7917 (mtm) cc_final: 0.7715 (mtm) REVERT: A 467 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7977 (mm) REVERT: D 486 GLU cc_start: 0.6780 (tp30) cc_final: 0.6346 (tp30) REVERT: E 65 ARG cc_start: 0.7216 (ptm160) cc_final: 0.6719 (ptm160) REVERT: E 85 GLU cc_start: 0.3038 (OUTLIER) cc_final: 0.2784 (mp0) REVERT: E 149 ASN cc_start: 0.8645 (t0) cc_final: 0.8298 (t0) REVERT: G 149 ASN cc_start: 0.8684 (t0) cc_final: 0.8427 (t0) outliers start: 46 outliers final: 25 residues processed: 334 average time/residue: 0.1363 time to fit residues: 69.7784 Evaluate side-chains 312 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain A residue 396 VAL 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 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 729 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 215 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS C 747 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.153813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.127470 restraints weight = 43924.219| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.17 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18863 Z= 0.170 Angle : 0.506 10.348 25517 Z= 0.266 Chirality : 0.040 0.139 2871 Planarity : 0.004 0.059 3147 Dihedral : 3.511 15.120 2555 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.78 % Allowed : 22.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.18), residues: 2331 helix: 2.76 (0.14), residues: 1375 sheet: -1.15 (0.37), residues: 172 loop : -0.61 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 65 TYR 0.013 0.001 TYR B 711 PHE 0.014 0.002 PHE F 201 TRP 0.014 0.002 TRP A 551 HIS 0.006 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00402 (18851) covalent geometry : angle 0.50474 (25493) SS BOND : bond 0.00277 ( 12) SS BOND : angle 1.23813 ( 24) hydrogen bonds : bond 0.04319 ( 1162) hydrogen bonds : angle 3.77328 ( 3415) *********************** 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 342 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1927 (OUTLIER) cc_final: 0.1536 (p0) REVERT: H 117 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7477 (mpp) REVERT: C 425 CYS cc_start: 0.8036 (m) cc_final: 0.7828 (m) REVERT: B 637 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: B 703 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 463 MET cc_start: 0.8017 (mtm) cc_final: 0.7699 (mtm) REVERT: A 467 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7942 (mm) REVERT: D 486 GLU cc_start: 0.6846 (tp30) cc_final: 0.6441 (tp30) REVERT: E 65 ARG cc_start: 0.7292 (ptm160) cc_final: 0.6714 (ptm160) REVERT: E 85 GLU cc_start: 0.3161 (OUTLIER) cc_final: 0.2804 (mp0) outliers start: 54 outliers final: 34 residues processed: 321 average time/residue: 0.1283 time to fit residues: 63.5736 Evaluate side-chains 316 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 121 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 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 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 E residue 11 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 141 optimal weight: 0.3980 chunk 212 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS C 747 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN E 160 ASN G 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.123983 restraints weight = 57264.257| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.35 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18863 Z= 0.105 Angle : 0.440 9.482 25517 Z= 0.231 Chirality : 0.038 0.124 2871 Planarity : 0.003 0.054 3147 Dihedral : 3.297 15.790 2555 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 22.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.18), residues: 2331 helix: 3.01 (0.14), residues: 1377 sheet: -1.18 (0.36), residues: 192 loop : -0.48 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 65 TYR 0.012 0.001 TYR B 711 PHE 0.011 0.001 PHE A 658 TRP 0.018 0.001 TRP D 766 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00231 (18851) covalent geometry : angle 0.43911 (25493) SS BOND : bond 0.00190 ( 12) SS BOND : angle 1.03367 ( 24) hydrogen bonds : bond 0.03626 ( 1162) hydrogen bonds : angle 3.52298 ( 3415) *********************** 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 346 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 293 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2010 (OUTLIER) cc_final: 0.1585 (p0) REVERT: H 117 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7389 (mpp) REVERT: H 131 ARG cc_start: 0.5316 (tpt-90) cc_final: 0.4136 (mtp180) REVERT: C 756 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.7103 (mt0) REVERT: B 637 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: B 703 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8041 (mp) REVERT: A 467 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8016 (mm) REVERT: D 412 HIS cc_start: 0.5896 (p-80) cc_final: 0.5477 (p-80) REVERT: D 486 GLU cc_start: 0.6707 (tp30) cc_final: 0.6345 (tp30) REVERT: E 65 ARG cc_start: 0.7262 (ptm160) cc_final: 0.6815 (ptm160) REVERT: E 85 GLU cc_start: 0.3165 (OUTLIER) cc_final: 0.2880 (mp0) REVERT: G 149 ASN cc_start: 0.8666 (t0) cc_final: 0.8437 (t0) outliers start: 53 outliers final: 37 residues processed: 331 average time/residue: 0.1345 time to fit residues: 68.8482 Evaluate side-chains 320 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 121 CYS Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 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 795 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 122 optimal weight: 0.0030 chunk 117 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 179 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.8392 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.157485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132726 restraints weight = 44184.528| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 4.09 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18863 Z= 0.097 Angle : 0.433 9.869 25517 Z= 0.227 Chirality : 0.037 0.124 2871 Planarity : 0.003 0.059 3147 Dihedral : 3.198 15.262 2555 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.57 % Allowed : 23.07 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.18), residues: 2331 helix: 3.13 (0.14), residues: 1377 sheet: -1.05 (0.38), residues: 172 loop : -0.54 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 65 TYR 0.013 0.001 TYR A 673 PHE 0.015 0.001 PHE A 438 TRP 0.018 0.001 TRP D 766 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00207 (18851) covalent geometry : angle 0.43235 (25493) SS BOND : bond 0.00249 ( 12) SS BOND : angle 0.87029 ( 24) hydrogen bonds : bond 0.03471 ( 1162) hydrogen bonds : angle 3.46340 ( 3415) *********************** 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 336 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 ARG cc_start: 0.6148 (ptt90) cc_final: 0.5339 (ptp-170) REVERT: H 86 ASP cc_start: 0.2124 (OUTLIER) cc_final: 0.1688 (p0) REVERT: H 117 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7411 (mpp) REVERT: H 131 ARG cc_start: 0.5292 (tpt-90) cc_final: 0.4056 (mtp180) REVERT: C 425 CYS cc_start: 0.7895 (m) cc_final: 0.7566 (m) REVERT: C 756 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7069 (mt0) REVERT: B 637 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6557 (pm20) REVERT: B 703 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 467 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8022 (mm) REVERT: D 412 HIS cc_start: 0.5810 (p-80) cc_final: 0.5390 (p-80) REVERT: D 486 GLU cc_start: 0.6708 (tp30) cc_final: 0.6273 (tp30) REVERT: E 65 ARG cc_start: 0.7270 (ptm160) cc_final: 0.6834 (ptm160) REVERT: E 85 GLU cc_start: 0.3076 (OUTLIER) cc_final: 0.2788 (mp0) REVERT: E 149 ASN cc_start: 0.8612 (t0) cc_final: 0.8377 (t0) outliers start: 50 outliers final: 35 residues processed: 320 average time/residue: 0.1428 time to fit residues: 70.4073 Evaluate side-chains 313 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP 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 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 399 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 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 666 VAL Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 231 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS C 747 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN E 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121640 restraints weight = 59530.439| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.38 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18863 Z= 0.151 Angle : 0.490 11.798 25517 Z= 0.256 Chirality : 0.039 0.134 2871 Planarity : 0.004 0.059 3147 Dihedral : 3.403 14.806 2555 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.68 % Allowed : 23.17 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.18), residues: 2331 helix: 2.85 (0.14), residues: 1375 sheet: -1.09 (0.38), residues: 172 loop : -0.61 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 65 TYR 0.014 0.001 TYR H 32 PHE 0.015 0.001 PHE A 659 TRP 0.017 0.001 TRP A 551 HIS 0.006 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00356 (18851) covalent geometry : angle 0.48961 (25493) SS BOND : bond 0.00439 ( 12) SS BOND : angle 0.97508 ( 24) hydrogen bonds : bond 0.04044 ( 1162) hydrogen bonds : angle 3.68206 ( 3415) *********************** 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: 52 poor density : 280 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2267 (OUTLIER) cc_final: 0.1819 (p0) REVERT: H 117 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7410 (mpp) REVERT: H 131 ARG cc_start: 0.5471 (tpt-90) cc_final: 0.4261 (mtp180) REVERT: F 31 ASP cc_start: 0.7826 (p0) cc_final: 0.7344 (p0) REVERT: F 65 ARG cc_start: 0.6285 (ptt-90) cc_final: 0.6075 (pmt-80) REVERT: C 425 CYS cc_start: 0.8017 (m) cc_final: 0.7713 (m) REVERT: C 756 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7094 (mt0) REVERT: B 416 GLU cc_start: 0.4698 (tp30) cc_final: 0.4347 (tt0) REVERT: B 637 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6497 (pm20) REVERT: B 703 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 467 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8012 (mm) REVERT: A 699 LYS cc_start: 0.7130 (mtpt) cc_final: 0.6706 (mttp) REVERT: D 486 GLU cc_start: 0.6845 (tp30) cc_final: 0.6453 (tp30) REVERT: E 65 ARG cc_start: 0.7304 (ptm160) cc_final: 0.6826 (ptm160) REVERT: E 85 GLU cc_start: 0.3233 (OUTLIER) cc_final: 0.2988 (mp0) REVERT: E 102 ARG cc_start: 0.8386 (tpt90) cc_final: 0.8163 (tpt90) outliers start: 52 outliers final: 39 residues processed: 316 average time/residue: 0.1502 time to fit residues: 72.0211 Evaluate side-chains 319 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 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 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 155 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 180 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 7 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 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 = 0.159863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135027 restraints weight = 48648.680| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.31 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18863 Z= 0.096 Angle : 0.446 11.864 25517 Z= 0.232 Chirality : 0.038 0.181 2871 Planarity : 0.003 0.056 3147 Dihedral : 3.209 15.451 2555 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.47 % Allowed : 23.43 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.18), residues: 2331 helix: 3.12 (0.14), residues: 1377 sheet: -1.07 (0.36), residues: 188 loop : -0.46 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 675 TYR 0.030 0.001 TYR B 673 PHE 0.014 0.001 PHE A 438 TRP 0.016 0.001 TRP D 766 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00203 (18851) covalent geometry : angle 0.44518 (25493) SS BOND : bond 0.00261 ( 12) SS BOND : angle 1.06480 ( 24) hydrogen bonds : bond 0.03416 ( 1162) hydrogen bonds : angle 3.44696 ( 3415) *********************** 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 334 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 ARG cc_start: 0.6027 (ptt90) cc_final: 0.5259 (ptp-170) REVERT: H 86 ASP cc_start: 0.2359 (OUTLIER) cc_final: 0.1890 (p0) REVERT: H 117 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7365 (mpp) REVERT: H 131 ARG cc_start: 0.5365 (tpt-90) cc_final: 0.4084 (mtp180) REVERT: C 425 CYS cc_start: 0.7904 (m) cc_final: 0.7600 (m) REVERT: C 756 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7068 (mt0) REVERT: B 416 GLU cc_start: 0.4744 (tp30) cc_final: 0.4413 (tt0) REVERT: B 637 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: B 703 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 467 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8010 (mm) REVERT: D 412 HIS cc_start: 0.5797 (p-80) cc_final: 0.5377 (p-80) REVERT: D 486 GLU cc_start: 0.6711 (tp30) cc_final: 0.6378 (tp30) REVERT: E 65 ARG cc_start: 0.7319 (ptm160) cc_final: 0.6941 (ptm160) REVERT: E 85 GLU cc_start: 0.3115 (OUTLIER) cc_final: 0.2800 (mp0) outliers start: 48 outliers final: 33 residues processed: 319 average time/residue: 0.1451 time to fit residues: 71.2943 Evaluate side-chains 315 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 502 ILE 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 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 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 85 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS 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 110 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 69 optimal weight: 0.0000 chunk 5 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.157869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.133072 restraints weight = 46997.090| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 4.18 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18863 Z= 0.100 Angle : 0.450 12.083 25517 Z= 0.234 Chirality : 0.038 0.180 2871 Planarity : 0.003 0.058 3147 Dihedral : 3.181 14.810 2555 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.06 % Allowed : 23.94 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.18), residues: 2331 helix: 3.12 (0.13), residues: 1377 sheet: -1.17 (0.36), residues: 192 loop : -0.47 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 65 TYR 0.028 0.001 TYR B 673 PHE 0.014 0.001 PHE A 438 TRP 0.015 0.001 TRP D 766 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00218 (18851) covalent geometry : angle 0.44914 (25493) SS BOND : bond 0.00214 ( 12) SS BOND : angle 1.03228 ( 24) hydrogen bonds : bond 0.03448 ( 1162) hydrogen bonds : angle 3.45830 ( 3415) ********************** 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 317 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 ARG cc_start: 0.5979 (ptt90) cc_final: 0.5197 (ptp-170) REVERT: H 86 ASP cc_start: 0.2335 (OUTLIER) cc_final: 0.1870 (p0) REVERT: H 117 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7385 (mpp) REVERT: H 131 ARG cc_start: 0.5309 (tpt-90) cc_final: 0.4057 (mtp180) REVERT: C 425 CYS cc_start: 0.7867 (m) cc_final: 0.7559 (m) REVERT: C 756 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.7029 (mt0) REVERT: B 416 GLU cc_start: 0.4684 (tp30) cc_final: 0.4347 (tt0) REVERT: B 637 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: B 703 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 467 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8031 (mm) REVERT: D 412 HIS cc_start: 0.5752 (p-80) cc_final: 0.5327 (p-80) REVERT: D 486 GLU cc_start: 0.6761 (tp30) cc_final: 0.6373 (tp30) REVERT: E 65 ARG cc_start: 0.7319 (ptm160) cc_final: 0.6907 (ptm160) REVERT: E 85 GLU cc_start: 0.3141 (OUTLIER) cc_final: 0.2818 (mp0) outliers start: 40 outliers final: 32 residues processed: 307 average time/residue: 0.1470 time to fit residues: 69.3091 Evaluate side-chains 310 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 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 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 85 GLU Chi-restraints excluded: chain E residue 155 VAL 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 110 optimal weight: 0.9990 chunk 163 optimal weight: 0.3980 chunk 159 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.158236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124270 restraints weight = 60643.260| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.41 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 18863 Z= 0.145 Angle : 0.657 59.153 25517 Z= 0.388 Chirality : 0.041 0.830 2871 Planarity : 0.004 0.087 3147 Dihedral : 3.217 24.026 2555 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.21 % Allowed : 23.79 % Favored : 74.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.18), residues: 2331 helix: 3.10 (0.13), residues: 1377 sheet: -1.16 (0.36), residues: 192 loop : -0.47 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 65 TYR 0.025 0.001 TYR B 673 PHE 0.013 0.001 PHE A 438 TRP 0.014 0.001 TRP D 766 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00283 (18851) covalent geometry : angle 0.65666 (25493) SS BOND : bond 0.00193 ( 12) SS BOND : angle 1.07698 ( 24) hydrogen bonds : bond 0.03486 ( 1162) hydrogen bonds : angle 3.47784 ( 3415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.02 seconds wall clock time: 57 minutes 31.78 seconds (3451.78 seconds total)