Starting phenix.real_space_refine on Sat Feb 7 12:43:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o80_70213/02_2026/9o80_70213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o80_70213/02_2026/9o80_70213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o80_70213/02_2026/9o80_70213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o80_70213/02_2026/9o80_70213.map" model { file = "/net/cci-nas-00/data/ceres_data/9o80_70213/02_2026/9o80_70213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o80_70213/02_2026/9o80_70213.cif" } resolution = 3.77 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= 0.000 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 228 5.16 5 C 21170 2.51 5 N 5340 2.21 5 O 5598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32336 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7919 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 991} Chain breaks: 8 Unresolved non-hydrogen bonds: 486 Unresolved non-hydrogen angles: 602 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 17, 'ARG:plan': 11, 'ASP:plan': 7, 'HIS:plan': 5, 'GLN:plan1': 12, 'ASN:plan1': 3, 'TYR:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 293 Chain: "A" Number of atoms: 7890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 7890 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1000} Chain breaks: 6 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 706 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 15, 'ASP:plan': 11, 'HIS:plan': 5, 'GLN:plan1': 14, 'TRP:plan': 1, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 364 Chain: "D" Number of atoms: 7798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 7798 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 995} Chain breaks: 6 Unresolved non-hydrogen bonds: 602 Unresolved non-hydrogen angles: 737 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 18, 'ASP:plan': 11, 'HIS:plan': 5, 'GLN:plan1': 15, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 383 Chain: "B" Number of atoms: 7889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 7889 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 589 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 491 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 26, 'ARG:plan': 17, 'ASP:plan': 11, 'HIS:plan': 5, 'GLN:plan1': 14, 'TRP:plan': 2, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 371 Chain: "C" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 280 Unusual residues: {'Y01': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.41, per 1000 atoms: 0.23 Number of scatterers: 32336 At special positions: 0 Unit cell: (152.81, 159.418, 158.592, 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 228 16.00 O 5598 8.00 N 5340 7.00 C 21170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1061 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1061 " distance=2.04 Simple disulfide: pdb=" SG CYS D1044 " - pdb=" SG CYS D1061 " distance=2.04 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1061 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7832 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 66.9% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'C' and resid 30 through 36 removed outlier: 3.709A pdb=" N PHE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 removed outlier: 3.984A pdb=" N HIS C 63 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 163 through 182 removed outlier: 3.591A pdb=" N LEU C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 206 removed outlier: 3.986A pdb=" N HIS C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.967A pdb=" N ILE C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 405 through 418 removed outlier: 4.206A pdb=" N ASN C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 removed outlier: 3.886A pdb=" N LEU C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 428 " --> pdb=" O GLN C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 440 Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 465 through 476 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 493 removed outlier: 3.929A pdb=" N LEU C 488 " --> pdb=" O THR C 484 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 512 Processing helix chain 'C' and resid 533 through 546 removed outlier: 3.539A pdb=" N LEU C 539 " --> pdb=" O ILE C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 563 Processing helix chain 'C' and resid 613 through 625 removed outlier: 4.042A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.564A pdb=" N HIS C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 661 Processing helix chain 'C' and resid 665 through 694 removed outlier: 3.801A pdb=" N SER C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 704 removed outlier: 3.531A pdb=" N LYS C 700 " --> pdb=" O GLN C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 removed outlier: 3.745A pdb=" N LEU C 717 " --> pdb=" O THR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 728 removed outlier: 3.545A pdb=" N ILE C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.654A pdb=" N ILE C 764 " --> pdb=" O PRO C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 846 removed outlier: 4.145A pdb=" N TYR C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 872 removed outlier: 3.623A pdb=" N TYR C 855 " --> pdb=" O LYS C 851 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 872 " --> pdb=" O TYR C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 901 Processing helix chain 'C' and resid 907 through 918 removed outlier: 4.317A pdb=" N GLU C 918 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 940 removed outlier: 3.698A pdb=" N VAL C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 968 removed outlier: 3.979A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 957 " --> pdb=" O CYS C 953 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 958 " --> pdb=" O VAL C 954 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 963 " --> pdb=" O TRP C 959 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1009 removed outlier: 4.573A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 990 " --> pdb=" O ASP C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1026 removed outlier: 3.561A pdb=" N LYS C1021 " --> pdb=" O TRP C1017 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET C1026 " --> pdb=" O ASN C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1031 removed outlier: 3.788A pdb=" N ILE C1031 " --> pdb=" O TYR C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1082 removed outlier: 3.969A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1120 removed outlier: 3.634A pdb=" N PHE C1096 " --> pdb=" O ASN C1092 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU C1097 " --> pdb=" O ASN C1093 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER C1100 " --> pdb=" O PHE C1096 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C1105 " --> pdb=" O ILE C1101 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C1120 " --> pdb=" O THR C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1139 removed outlier: 4.367A pdb=" N ILE C1129 " --> pdb=" O PRO C1125 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE C1130 " --> pdb=" O PRO C1126 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER C1131 " --> pdb=" O LEU C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1191 Processing helix chain 'C' and resid 1192 through 1231 removed outlier: 3.576A pdb=" N ILE C1230 " --> pdb=" O GLN C1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.570A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 180 Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.605A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.981A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.751A pdb=" N ASP A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 371 through 386 Processing helix chain 'A' and resid 404 through 418 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 501 through 514 removed outlier: 3.572A pdb=" N LEU A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 546 removed outlier: 3.870A pdb=" N GLY A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'A' and resid 555 through 565 removed outlier: 3.696A pdb=" N HIS A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 625 removed outlier: 4.182A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.956A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 662 removed outlier: 3.620A pdb=" N LYS A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.871A pdb=" N SER A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.788A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.636A pdb=" N MET A 741 " --> pdb=" O THR A 737 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 760 Processing helix chain 'A' and resid 761 through 767 removed outlier: 4.019A pdb=" N LEU A 765 " --> pdb=" O PRO A 761 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 843 Processing helix chain 'A' and resid 844 through 847 Processing helix chain 'A' and resid 849 through 872 removed outlier: 4.000A pdb=" N TYR A 855 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 902 removed outlier: 3.710A pdb=" N VAL A 885 " --> pdb=" O GLN A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 917 Processing helix chain 'A' and resid 918 through 940 removed outlier: 3.735A pdb=" N VAL A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 962 removed outlier: 4.038A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 957 " --> pdb=" O CYS A 953 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 968 removed outlier: 3.927A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1009 removed outlier: 4.473A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1026 removed outlier: 3.519A pdb=" N LYS A1021 " --> pdb=" O TRP A1017 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1036 through 1040 removed outlier: 3.703A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1081 removed outlier: 4.241A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1094 through 1120 removed outlier: 4.524A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1140 Processing helix chain 'A' and resid 1163 through 1190 Processing helix chain 'A' and resid 1192 through 1231 Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.547A pdb=" N PHE D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 63 removed outlier: 4.089A pdb=" N HIS D 63 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 140 removed outlier: 3.697A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 182 removed outlier: 3.671A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 209 removed outlier: 3.529A pdb=" N HIS D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.907A pdb=" N ILE D 223 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 224 " --> pdb=" O TRP D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 224' Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 273 through 287 Processing helix chain 'D' and resid 308 through 319 removed outlier: 4.123A pdb=" N SER D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 removed outlier: 3.579A pdb=" N TYR D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 368 Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.762A pdb=" N THR D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 429 Processing helix chain 'D' and resid 433 through 439 removed outlier: 3.952A pdb=" N ALA D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 465 through 475 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 484 through 493 removed outlier: 3.709A pdb=" N ASN D 493 " --> pdb=" O GLU D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 513 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 555 through 565 removed outlier: 3.734A pdb=" N LEU D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 625 removed outlier: 3.818A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.558A pdb=" N HIS D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'D' and resid 665 through 694 removed outlier: 3.665A pdb=" N SER D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 704 Processing helix chain 'D' and resid 713 through 721 Processing helix chain 'D' and resid 723 through 728 Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.574A pdb=" N GLY D 742 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 removed outlier: 4.587A pdb=" N LYS D 753 " --> pdb=" O ASN D 749 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 755 " --> pdb=" O GLY D 751 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 759 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 760 " --> pdb=" O LEU D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 767 removed outlier: 3.619A pdb=" N LEU D 767 " --> pdb=" O ILE D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 845 Processing helix chain 'D' and resid 847 through 872 Processing helix chain 'D' and resid 879 through 902 Processing helix chain 'D' and resid 907 through 916 Processing helix chain 'D' and resid 918 through 940 removed outlier: 4.003A pdb=" N VAL D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR D 923 " --> pdb=" O TYR D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 962 removed outlier: 4.229A pdb=" N ILE D 957 " --> pdb=" O CYS D 953 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR D 958 " --> pdb=" O VAL D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 968 removed outlier: 4.111A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 1009 removed outlier: 4.726A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1025 removed outlier: 3.867A pdb=" N LYS D1021 " --> pdb=" O TRP D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1026 through 1031 removed outlier: 3.721A pdb=" N MET D1030 " --> pdb=" O MET D1026 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D1031 " --> pdb=" O PRO D1027 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1026 through 1031' Processing helix chain 'D' and resid 1036 through 1040 removed outlier: 3.532A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1082 removed outlier: 4.042A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1082 through 1120 removed outlier: 3.760A pdb=" N THR D1094 " --> pdb=" O VAL D1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D1095 " --> pdb=" O PHE D1091 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D1096 " --> pdb=" O ASN D1092 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU D1097 " --> pdb=" O ASN D1093 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1135 Processing helix chain 'D' and resid 1138 through 1142 removed outlier: 3.849A pdb=" N CYS D1142 " --> pdb=" O HIS D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1190 removed outlier: 4.395A pdb=" N LYS D1169 " --> pdb=" O ASP D1165 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL D1170 " --> pdb=" O GLU D1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1232 removed outlier: 3.567A pdb=" N ARG D1196 " --> pdb=" O SER D1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 59 through 63 removed outlier: 4.230A pdb=" N HIS B 63 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.796A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 180 Processing helix chain 'B' and resid 193 through 207 removed outlier: 3.721A pdb=" N SER B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.008A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 404 through 418 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 440 removed outlier: 3.828A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 476 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 514 Processing helix chain 'B' and resid 533 through 546 Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.557A pdb=" N THR B 554 " --> pdb=" O CYS B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 555 through 564 removed outlier: 3.640A pdb=" N ARG B 559 " --> pdb=" O ARG B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 625 removed outlier: 4.224A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 removed outlier: 3.644A pdb=" N HIS B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.568A pdb=" N SER B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 704 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 728 removed outlier: 3.914A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 728 " --> pdb=" O ARG B 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 723 through 728' Processing helix chain 'B' and resid 729 through 741 Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.790A pdb=" N VAL B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 835 through 846 removed outlier: 4.362A pdb=" N ARG B 839 " --> pdb=" O ILE B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 872 removed outlier: 3.615A pdb=" N TYR B 855 " --> pdb=" O LYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 902 Processing helix chain 'B' and resid 907 through 916 Processing helix chain 'B' and resid 918 through 939 removed outlier: 3.664A pdb=" N VAL B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 962 removed outlier: 3.745A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B 957 " --> pdb=" O CYS B 953 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 958 " --> pdb=" O VAL B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 968 removed outlier: 3.759A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1009 removed outlier: 3.928A pdb=" N TYR B 976 " --> pdb=" O TYR B 972 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1029 removed outlier: 4.305A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N MET B1026 " --> pdb=" O ASN B1022 " (cutoff:3.500A) Proline residue: B1027 - end of helix Processing helix chain 'B' and resid 1036 through 1040 removed outlier: 3.665A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1080 removed outlier: 4.004A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1094 Processing helix chain 'B' and resid 1094 through 1120 removed outlier: 4.426A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1127 Processing helix chain 'B' and resid 1128 through 1145 Processing helix chain 'B' and resid 1163 through 1192 Processing helix chain 'B' and resid 1192 through 1231 removed outlier: 3.520A pdb=" N ARG B1196 " --> pdb=" O SER B1192 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.900A pdb=" N GLU C 40 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C 99 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.598A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA C 105 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 123 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE C 185 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE C 218 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C 187 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU C 150 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU C 302 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER C 152 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL C 327 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 301 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 240 removed outlier: 8.162A pdb=" N PHE A 106 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 236 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 108 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU A 110 " --> pdb=" O PRO A 238 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN A 240 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN A 112 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA A 105 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 120 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET A 121 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU A 261 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL A 123 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP A 263 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 125 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.655A pdb=" N CYS A 329 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 395 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 328 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 37 through 40 Processing sheet with id=AA7, first strand: chain 'D' and resid 232 through 240 removed outlier: 5.802A pdb=" N THR D 108 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D 236 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU D 110 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN D 112 " --> pdb=" O PRO D 238 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLN D 240 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.714A pdb=" N VAL D 125 " --> pdb=" O ASP D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 186 removed outlier: 7.875A pdb=" N VAL D 327 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA D 301 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N CYS D 329 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE D 303 " --> pdb=" O CYS D 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 239 removed outlier: 4.374A pdb=" N TYR B 239 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET B 121 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.206A pdb=" N VAL B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) 1947 hydrogen bonds defined for protein. 5757 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5723 1.33 - 1.45: 8518 1.45 - 1.58: 18501 1.58 - 1.71: 3 1.71 - 1.84: 381 Bond restraints: 33126 Sorted by residual: bond pdb=" C PRO B 761 " pdb=" N PRO B 762 " ideal model delta sigma weight residual 1.335 1.420 -0.085 1.19e-02 7.06e+03 5.10e+01 bond pdb=" C PRO D 761 " pdb=" N PRO D 762 " ideal model delta sigma weight residual 1.335 1.420 -0.086 1.28e-02 6.10e+03 4.50e+01 bond pdb=" C PRO C 761 " pdb=" N PRO C 762 " ideal model delta sigma weight residual 1.334 1.388 -0.054 8.40e-03 1.42e+04 4.18e+01 bond pdb=" C GLU C 904 " pdb=" N PRO C 905 " ideal model delta sigma weight residual 1.332 1.404 -0.072 1.30e-02 5.92e+03 3.11e+01 bond pdb=" C ILE D 835 " pdb=" N PRO D 836 " ideal model delta sigma weight residual 1.335 1.404 -0.068 1.36e-02 5.41e+03 2.51e+01 ... (remaining 33121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 42877 2.83 - 5.65: 1903 5.65 - 8.48: 336 8.48 - 11.30: 63 11.30 - 14.13: 13 Bond angle restraints: 45192 Sorted by residual: angle pdb=" C PRO D1124 " pdb=" CA PRO D1124 " pdb=" CB PRO D1124 " ideal model delta sigma weight residual 110.92 121.26 -10.34 1.22e+00 6.72e-01 7.19e+01 angle pdb=" N VAL C 477 " pdb=" CA VAL C 477 " pdb=" C VAL C 477 " ideal model delta sigma weight residual 113.20 106.55 6.65 9.60e-01 1.09e+00 4.80e+01 angle pdb=" C ILE D1067 " pdb=" N VAL D1068 " pdb=" CA VAL D1068 " ideal model delta sigma weight residual 120.24 124.58 -4.34 6.30e-01 2.52e+00 4.75e+01 angle pdb=" C ILE B1067 " pdb=" N VAL B1068 " pdb=" CA VAL B1068 " ideal model delta sigma weight residual 120.24 124.30 -4.06 6.30e-01 2.52e+00 4.14e+01 angle pdb=" N ILE D1128 " pdb=" CA ILE D1128 " pdb=" C ILE D1128 " ideal model delta sigma weight residual 111.45 105.51 5.94 9.30e-01 1.16e+00 4.08e+01 ... (remaining 45187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 19575 24.77 - 49.54: 1000 49.54 - 74.31: 146 74.31 - 99.08: 25 99.08 - 123.85: 9 Dihedral angle restraints: 20755 sinusoidal: 8657 harmonic: 12098 Sorted by residual: dihedral pdb=" CB CYS C1044 " pdb=" SG CYS C1044 " pdb=" SG CYS C1061 " pdb=" CB CYS C1061 " ideal model delta sinusoidal sigma weight residual -86.00 -149.75 63.75 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CA MET C 255 " pdb=" C MET C 255 " pdb=" N HIS C 256 " pdb=" CA HIS C 256 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA MET C 121 " pdb=" C MET C 121 " pdb=" N TYR C 122 " pdb=" CA TYR C 122 " ideal model delta harmonic sigma weight residual -180.00 -154.22 -25.78 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 20752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4295 0.085 - 0.171: 858 0.171 - 0.256: 98 0.256 - 0.341: 20 0.341 - 0.426: 8 Chirality restraints: 5279 Sorted by residual: chirality pdb=" CG LEU D 488 " pdb=" CB LEU D 488 " pdb=" CD1 LEU D 488 " pdb=" CD2 LEU D 488 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU B 483 " pdb=" CB LEU B 483 " pdb=" CD1 LEU B 483 " pdb=" CD2 LEU B 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CG LEU C 765 " pdb=" CB LEU C 765 " pdb=" CD1 LEU C 765 " pdb=" CD2 LEU C 765 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 5276 not shown) Planarity restraints: 5555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1029 " 0.045 2.00e-02 2.50e+03 3.20e-02 2.57e+01 pdb=" CG TRP C1029 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP C1029 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C1029 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1029 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C1029 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C1029 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1029 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1029 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C1029 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 853 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C TRP A 853 " 0.076 2.00e-02 2.50e+03 pdb=" O TRP A 853 " -0.028 2.00e-02 2.50e+03 pdb=" N PHE A 854 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 853 " 0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C TRP D 853 " -0.074 2.00e-02 2.50e+03 pdb=" O TRP D 853 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE D 854 " 0.025 2.00e-02 2.50e+03 ... (remaining 5552 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8052 2.81 - 3.33: 32639 3.33 - 3.86: 53335 3.86 - 4.38: 61853 4.38 - 4.90: 101361 Nonbonded interactions: 257240 Sorted by model distance: nonbonded pdb=" O PHE A1130 " pdb=" OG1 THR A1134 " model vdw 2.289 3.040 nonbonded pdb=" O LEU C 706 " pdb=" CD1 LEU C 706 " model vdw 2.319 3.460 nonbonded pdb=" O PRO D1011 " pdb=" OD1 ASN D1012 " model vdw 2.323 3.040 nonbonded pdb=" O ALA D1020 " pdb=" N ILE D1023 " model vdw 2.380 3.120 nonbonded pdb=" CB MET A1133 " pdb=" CE MET A1133 " model vdw 2.399 3.088 ... (remaining 257235 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 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 137 or (resid 138 and (name N or name CA or n \ ame C or name O or name CB )) or resid 139 through 207 or resid 213 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 232 or (resid 233 and (name N or name CA or name C or name O or name \ CB )) or resid 234 through 259 or (resid 260 and (name N or name CA or name C o \ r name O or name CB )) or resid 261 through 269 or (resid 270 and (name N or nam \ e CA or name C or name O or name CB )) or resid 271 through 301 or (resid 302 an \ d (name N or name CA or name C or name O or name CB )) or resid 303 through 342 \ or (resid 343 and (name N or name CA or name C or name O or name CB )) or resid \ 344 through 369 or (resid 370 and (name N or name CA or name C or name O or name \ CB )) or resid 371 through 385 or (resid 386 through 387 and (name N or name CA \ or name C or name O or name CB )) or resid 388 through 398 or resid 403 or (res \ id 404 and (name N or name CA or name C or name O or name CB )) or resid 405 thr \ ough 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 419 or (resid 420 through 421 and (name N or name CA or nam \ e C or name O or name CB )) or resid 422 through 441 or (resid 442 through 444 a \ nd (name N or name CA or name C or name O or name CB )) or resid 445 through 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 through 451 or (resid 452 and (name N or name CA or name C or name O or nam \ e CB )) or resid 453 through 457 or (resid 458 and (name N or name CA or name C \ or name O or name CB )) or resid 459 through 488 or (resid 489 through 490 and ( \ name N or name CA or name C or name O or name CB )) or resid 491 through 498 or \ (resid 499 through 500 and (name N or name CA or name C or name O or name CB )) \ or resid 501 through 509 or (resid 510 through 514 and (name N or name CA or nam \ e C or name O or name CB )) or resid 531 through 629 or (resid 630 through 631 a \ nd (name N or name CA or name C or name O or name CB )) or resid 632 through 676 \ or (resid 677 and (name N or name CA or name C or name O or name CB )) or resid \ 678 through 744 or (resid 745 through 748 and (name N or name CA or name C or n \ ame O or name CB )) or resid 749 through 751 or (resid 752 and (name N or name C \ A or name C or name O or name CB )) or resid 753 through 771 or resid 834 throug \ h 873 or (resid 874 and (name N or name CA or name C or name O or name CB )) or \ resid 875 or (resid 876 and (name N or name CA or name C or name O or name CB )) \ or resid 877 through 934 or (resid 935 and (name N or name CA or name C or name \ O or name CB )) or resid 936 through 937 or (resid 938 and (name N or name CA o \ r name C or name O or name CB )) or resid 939 through 955 or (resid 956 and (nam \ e N or name CA or name C or name O or name CB )) or resid 957 through 1025 or (r \ esid 1026 and (name N or name CA or name C or name O or name CB )) or resid 1027 \ through 1047 or resid 1058 through 1132 or (resid 1133 and (name N or name CA o \ r name C or name O or name CB )) or resid 1134 through 1138 or (resid 1139 and ( \ name N or name CA or name C or name O or name CB )) or resid 1140 through 1201 o \ r (resid 1202 and (name N or name CA or name C or name O or name CB )) or resid \ 1203 through 1204 or (resid 1205 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1206 through 1209 or (resid 1210 and (name N or name CA or na \ me C or name O or name CB )) or resid 1211 through 1405)) selection = (chain 'B' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 137 or (resid 138 and (name N or name CA or n \ ame C or name O or name CB )) or resid 139 through 207 or resid 213 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 269 or (resid 270 and (name N or name CA or name C o \ r name O or name CB )) or resid 271 through 301 or (resid 302 and (name N or nam \ e CA or name C or name O or name CB )) or resid 303 through 342 or (resid 343 an \ d (name N or name CA or name C or name O or name CB )) or resid 344 through 369 \ or (resid 370 and (name N or name CA or name C or name O or name CB )) or resid \ 371 through 385 or (resid 386 through 387 and (name N or name CA or name C or na \ me O or name CB )) or resid 388 through 398 or resid 403 or (resid 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 419 or (res \ id 420 through 421 and (name N or name CA or name C or name O or name CB )) or r \ esid 422 through 437 or (resid 438 and (name N or name CA or name C or name O or \ name CB )) or resid 439 through 441 or (resid 442 through 444 and (name N or na \ me CA or name C or name O or name CB )) or resid 445 through 447 or (resid 448 a \ nd (name N or name CA or name C or name O or name CB )) or resid 449 through 451 \ or (resid 452 and (name N or name CA or name C or name O or name CB )) or resid \ 453 through 457 or (resid 458 and (name N or name CA or name C or name O or nam \ e CB )) or resid 459 through 488 or (resid 489 through 490 and (name N or name C \ A or name C or name O or name CB )) or resid 491 through 498 or (resid 499 throu \ gh 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 509 or (resid 510 through 514 and (name N or name CA or name C or name O or \ name CB )) or resid 531 through 549 or (resid 550 and (name N or name CA or nam \ e C or name O or name CB )) or resid 551 through 676 or (resid 677 and (name N o \ r name CA or name C or name O or name CB )) or resid 678 through 873 or (resid 8 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 875 or (res \ id 876 and (name N or name CA or name C or name O or name CB )) or resid 877 thr \ ough 894 or (resid 895 and (name N or name CA or name C or name O or name CB )) \ or resid 896 through 934 or (resid 935 and (name N or name CA or name C or name \ O or name CB )) or resid 936 through 937 or (resid 938 and (name N or name CA or \ name C or name O or name CB )) or resid 939 through 955 or (resid 956 and (name \ N or name CA or name C or name O or name CB )) or resid 957 through 1025 or (re \ sid 1026 and (name N or name CA or name C or name O or name CB )) or resid 1027 \ through 1047 or resid 1058 through 1127 or (resid 1128 and (name N or name CA or \ name C or name O or name CB )) or resid 1129 through 1132 or (resid 1133 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1134 through 1138 or \ (resid 1139 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 140 through 1141 or resid 1158 through 1201 or (resid 1202 and (name N or name C \ A or name C or name O or name CB )) or resid 1203 through 1204 or (resid 1205 an \ d (name N or name CA or name C or name O or name CB )) or resid 1206 through 120 \ 9 or (resid 1210 and (name N or name CA or name C or name O or name CB )) or res \ id 1211 or (resid 1212 through 1213 and (name N or name CA or name C or name O o \ r name CB )) or resid 1214 through 1217 or (resid 1218 through 1232 and (name N \ or name CA or name C or name O or name CB )) or resid 1401 through 1405)) selection = (chain 'C' and (resid 30 through 203 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB )) or resid 205 through 232 or (resid 233 and (name N o \ r name CA or name C or name O or name CB )) or resid 234 through 254 or (resid 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 434 or (resid 435 and (name N or name CA or name C or name O or name CB )) or r \ esid 436 through 437 or (resid 438 and (name N or name CA or name C or name O or \ name CB )) or resid 439 through 441 or (resid 442 through 444 and (name N or na \ me CA or name C or name O or name CB )) or resid 445 through 446 or (resid 447 t \ hrough 448 and (name N or name CA or name C or name O or name CB )) or resid 449 \ through 457 or (resid 458 and (name N or name CA or name C or name O or name CB \ )) or resid 459 through 473 or (resid 474 and (name N or name CA or name C or n \ ame O or name CB )) or resid 475 through 480 or (resid 481 and (name N or name C \ A or name C or name O or name CB )) or resid 482 through 489 or (resid 490 and ( \ name N or name CA or name C or name O or name CB )) or resid 491 through 494 or \ (resid 495 and (name N or name CA or name C or name O or name CB )) or resid 496 \ through 499 or (resid 500 and (name N or name CA or name C or name O or name CB \ )) or resid 501 through 511 or (resid 512 through 514 and (name N or name CA or \ name C or name O or name CB )) or resid 531 through 535 or (resid 536 and (name \ N or name CA or name C or name O or name CB )) or resid 537 through 549 or (res \ id 550 and (name N or name CA or name C or name O or name CB )) or resid 551 thr \ ough 562 or (resid 563 through 608 and (name N or name CA or name C or name O or \ name CB )) or resid 609 through 628 or (resid 629 through 631 and (name N or na \ me CA or name C or name O or name CB )) or resid 632 through 660 or (resid 661 a \ nd (name N or name CA or name C or name O or name CB )) or resid 662 through 663 \ or (resid 664 through 667 and (name N or name CA or name C or name O or name CB \ )) or resid 668 through 676 or (resid 677 and (name N or name CA or name C or n \ ame O or name CB )) or resid 678 through 744 or (resid 745 through 748 and (name \ N or name CA or name C or name O or name CB )) or resid 749 through 751 or (res \ id 752 and (name N or name CA or name C or name O or name CB )) or resid 753 thr \ ough 759 or (resid 760 and (name N or name CA or name C or name O or name CB )) \ or resid 761 through 767 or (resid 768 and (name N or name CA or name C or name \ O or name CB )) or resid 769 through 770 or (resid 771 through 835 and (name N o \ r name CA or name C or name O or name CB )) or resid 836 or (resid 837 and (name \ N or name CA or name C or name O or name CB )) or resid 838 or (resid 839 and ( \ name N or name CA or name C or name O or name CB )) or resid 840 through 842 or \ (resid 843 and (name N or name CA or name C or name O or name CB )) or resid 844 \ through 873 or (resid 874 and (name N or name CA or name C or name O or name CB \ )) or resid 875 or (resid 876 and (name N or name CA or name C or name O or nam \ e CB )) or resid 877 through 894 or (resid 895 and (name N or name CA or name C \ or name O or name CB )) or resid 896 through 903 or (resid 904 and (name N or na \ me CA or name C or name O or name CB )) or resid 905 through 917 or (resid 918 a \ nd (name N or name CA or name C or name O or name CB )) or resid 919 through 937 \ or (resid 938 and (name N or name CA or name C or name O or name CB )) or resid \ 939 through 1017 or (resid 1018 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1019 through 1025 or (resid 1026 and (name N or name CA or na \ me C or name O or name CB )) or resid 1027 through 1047 or resid 1058 through 11 \ 11 or (resid 1112 and (name N or name CA or name C or name O or name CB )) or re \ sid 1113 through 1118 or (resid 1119 and (name N or name CA or name C or name O \ or name CB )) or resid 1120 through 1127 or (resid 1128 and (name N or name CA o \ r name C or name O or name CB )) or resid 1129 through 1141 or resid 1158 throug \ h 1167 or (resid 1168 and (name N or name CA or name C or name O or name CB )) o \ r resid 1169 through 1194 or (resid 1195 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1196 through 1209 or (resid 1210 and (name N or name \ CA or name C or name O or name CB )) or resid 1211 or (resid 1212 through 1213 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1214 through 12 \ 17 or (resid 1218 through 1232 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1401 through 1405)) selection = (chain 'D' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 137 or (resid 138 and (name N or name CA or n \ ame C or name O or name CB )) or resid 139 through 207 or resid 213 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 232 or (resid 233 and (name N or name CA or name C or name O or name \ CB )) or resid 234 through 259 or (resid 260 and (name N or name CA or name C o \ r name O or name CB )) or resid 261 through 269 or (resid 270 and (name N or nam \ e CA or name C or name O or name CB )) or resid 271 through 301 or (resid 302 an \ d (name N or name CA or name C or name O or name CB )) or resid 303 through 342 \ or (resid 343 and (name N or name CA or name C or name O or name CB )) or resid \ 344 through 369 or (resid 370 and (name N or name CA or name C or name O or name \ CB )) or resid 371 through 385 or (resid 386 through 387 and (name N or name CA \ or name C or name O or name CB )) or resid 388 through 398 or resid 403 or (res \ id 404 and (name N or name CA or name C or name O or name CB )) or resid 405 thr \ ough 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 419 or (resid 420 through 421 and (name N or name CA or nam \ e C or name O or name CB )) or resid 422 through 437 or (resid 438 and (name N o \ r name CA or name C or name O or name CB )) or resid 439 through 451 or (resid 4 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 453 through \ 488 or (resid 489 through 490 and (name N or name CA or name C or name O or nam \ e CB )) or resid 491 through 498 or (resid 499 through 500 and (name N or name C \ A or name C or name O or name CB )) or resid 501 through 509 or (resid 510 throu \ gh 530 and (name N or name CA or name C or name O or name CB )) or resid 531 thr \ ough 549 or (resid 550 and (name N or name CA or name C or name O or name CB )) \ or resid 551 through 629 or (resid 630 through 631 and (name N or name CA or nam \ e C or name O or name CB )) or resid 632 through 751 or (resid 752 and (name N o \ r name CA or name C or name O or name CB )) or resid 753 through 894 or (resid 8 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 896 through \ 934 or (resid 935 and (name N or name CA or name C or name O or name CB )) or r \ esid 936 through 955 or (resid 956 and (name N or name CA or name C or name O or \ name CB )) or resid 957 through 1047 or resid 1058 through 1127 or (resid 1128 \ and (name N or name CA or name C or name O or name CB )) or resid 1129 through 1 \ 132 or (resid 1133 and (name N or name CA or name C or name O or name CB )) or r \ esid 1134 through 1138 or (resid 1139 and (name N or name CA or name C or name O \ or name CB )) or resid 1140 through 1141 or resid 1158 through 1201 or (resid 1 \ 202 and (name N or name CA or name C or name O or name CB )) or resid 1203 throu \ gh 1204 or (resid 1205 and (name N or name CA or name C or name O or name CB )) \ or resid 1206 through 1405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.210 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.007 0.128 33130 Z= 0.405 Angle : 1.349 14.127 45200 Z= 0.763 Chirality : 0.070 0.426 5279 Planarity : 0.010 0.128 5555 Dihedral : 14.593 123.852 12911 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.20 % Favored : 94.70 % Rotamer: Outliers : 0.99 % Allowed : 1.02 % Favored : 97.99 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: -2.76 (0.11), residues: 4094 helix: -1.52 (0.09), residues: 2554 sheet: -1.53 (0.31), residues: 246 loop : -2.18 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG A 938 TYR 0.063 0.004 TYR D 862 PHE 0.060 0.004 PHE B1001 TRP 0.083 0.005 TRP C1029 HIS 0.014 0.002 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00744 (33126) covalent geometry : angle 1.34859 (45192) SS BOND : bond 0.00646 ( 4) SS BOND : angle 1.72577 ( 8) hydrogen bonds : bond 0.14163 ( 1947) hydrogen bonds : angle 6.83458 ( 5757) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 577 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TRP cc_start: 0.7688 (m-10) cc_final: 0.6994 (m-10) REVERT: C 176 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8958 (tmtt) REVERT: C 344 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8066 (ptpp) REVERT: C 453 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8102 (tp) REVERT: C 566 PHE cc_start: 0.6966 (m-80) cc_final: 0.6630 (m-10) REVERT: C 722 LYS cc_start: 0.9140 (mttm) cc_final: 0.8823 (tptp) REVERT: C 743 ARG cc_start: 0.7270 (tpm170) cc_final: 0.6608 (tpp-160) REVERT: C 874 MET cc_start: 0.8465 (ptp) cc_final: 0.8142 (ptp) REVERT: C 984 MET cc_start: 0.8600 (mmm) cc_final: 0.8395 (mmm) REVERT: C 987 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8585 (tpp) REVERT: C 1023 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8272 (mt) REVERT: C 1119 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7789 (tm-30) REVERT: C 1179 GLU cc_start: 0.8487 (tt0) cc_final: 0.7988 (tp30) REVERT: C 1184 GLU cc_start: 0.8733 (tp30) cc_final: 0.8500 (tp30) REVERT: C 1209 MET cc_start: 0.8887 (mmm) cc_final: 0.8442 (mtt) REVERT: A 37 TYR cc_start: 0.8004 (m-10) cc_final: 0.7175 (p90) REVERT: A 121 MET cc_start: 0.8289 (mmm) cc_final: 0.7884 (tpt) REVERT: A 223 ILE cc_start: 0.8818 (tp) cc_final: 0.8548 (mt) REVERT: A 280 LEU cc_start: 0.9124 (tp) cc_final: 0.8788 (tt) REVERT: A 722 LYS cc_start: 0.9113 (mttp) cc_final: 0.8813 (mmtm) REVERT: A 1102 SER cc_start: 0.8966 (t) cc_final: 0.8735 (p) REVERT: D 138 MET cc_start: 0.8985 (mmt) cc_final: 0.8596 (tpp) REVERT: D 176 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8857 (tttp) REVERT: D 457 MET cc_start: 0.8608 (mmt) cc_final: 0.8343 (mmt) REVERT: D 465 ARG cc_start: 0.7125 (mmp-170) cc_final: 0.6049 (mmm160) REVERT: D 543 TYR cc_start: 0.8799 (t80) cc_final: 0.8594 (t80) REVERT: D 744 LEU cc_start: 0.9131 (mt) cc_final: 0.8918 (tp) REVERT: D 902 MET cc_start: 0.7707 (mmt) cc_final: 0.6720 (mtt) REVERT: D 978 MET cc_start: 0.8641 (mpp) cc_final: 0.8329 (mtm) REVERT: D 1032 TYR cc_start: 0.8916 (m-80) cc_final: 0.8527 (m-80) REVERT: D 1102 SER cc_start: 0.9120 (m) cc_final: 0.8633 (p) REVERT: B 136 HIS cc_start: 0.8523 (m-70) cc_final: 0.8280 (m90) REVERT: B 429 LEU cc_start: 0.9269 (mm) cc_final: 0.8834 (pp) REVERT: B 625 MET cc_start: 0.9039 (mmm) cc_final: 0.8639 (mmt) REVERT: B 639 GLU cc_start: 0.8272 (mp0) cc_final: 0.7842 (mp0) REVERT: B 655 MET cc_start: 0.9326 (mtp) cc_final: 0.9039 (mtt) REVERT: B 671 GLU cc_start: 0.8575 (tp30) cc_final: 0.8236 (tp30) REVERT: B 682 LEU cc_start: 0.9575 (mt) cc_final: 0.9235 (mp) REVERT: B 855 TYR cc_start: 0.8126 (t80) cc_final: 0.7617 (t80) REVERT: B 895 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 995 LEU cc_start: 0.9287 (tt) cc_final: 0.9064 (tt) REVERT: B 1127 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8261 (tp) REVERT: B 1135 MET cc_start: 0.8175 (mtp) cc_final: 0.7816 (ptt) REVERT: B 1184 GLU cc_start: 0.8727 (tp30) cc_final: 0.8384 (tp30) outliers start: 31 outliers final: 7 residues processed: 598 average time/residue: 0.1872 time to fit residues: 186.2955 Evaluate side-chains 423 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 412 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1023 ILE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain A residue 1141 CYS Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 0.0470 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 HIS ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 GLN C1092 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A1092 ASN A1093 ASN A1139 HIS D 446 GLN ** D 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.096848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.075154 restraints weight = 114839.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.077773 restraints weight = 53519.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079419 restraints weight = 32566.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.080515 restraints weight = 23502.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.081220 restraints weight = 18905.428| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33130 Z= 0.148 Angle : 0.680 9.245 45200 Z= 0.352 Chirality : 0.042 0.220 5279 Planarity : 0.006 0.084 5555 Dihedral : 9.308 87.548 6149 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.93 % Favored : 95.95 % Rotamer: Outliers : 1.72 % Allowed : 7.39 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: -1.10 (0.12), residues: 4094 helix: -0.08 (0.10), residues: 2568 sheet: -1.27 (0.33), residues: 239 loop : -1.79 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 555 TYR 0.024 0.002 TYR B 530 PHE 0.022 0.002 PHE B1182 TRP 0.026 0.002 TRP A 915 HIS 0.012 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00308 (33126) covalent geometry : angle 0.67996 (45192) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.63217 ( 8) hydrogen bonds : bond 0.05254 ( 1947) hydrogen bonds : angle 4.90868 ( 5757) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 460 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TRP cc_start: 0.7444 (m-10) cc_final: 0.7114 (m100) REVERT: C 429 LEU cc_start: 0.9091 (mt) cc_final: 0.8744 (pp) REVERT: C 442 PHE cc_start: 0.8814 (t80) cc_final: 0.8506 (m-10) REVERT: C 453 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8001 (tp) REVERT: C 566 PHE cc_start: 0.6510 (m-80) cc_final: 0.6028 (m-10) REVERT: C 722 LYS cc_start: 0.9054 (mttm) cc_final: 0.8784 (tptp) REVERT: C 854 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8556 (t80) REVERT: C 987 MET cc_start: 0.8842 (ttm) cc_final: 0.8379 (tpp) REVERT: C 1179 GLU cc_start: 0.8471 (tt0) cc_final: 0.8000 (tp30) REVERT: C 1184 GLU cc_start: 0.8516 (tp30) cc_final: 0.8243 (tp30) REVERT: C 1187 ASP cc_start: 0.8168 (p0) cc_final: 0.7872 (p0) REVERT: A 37 TYR cc_start: 0.7679 (m-10) cc_final: 0.7024 (p90) REVERT: A 121 MET cc_start: 0.8161 (mmm) cc_final: 0.7734 (tpp) REVERT: A 223 ILE cc_start: 0.8690 (tp) cc_final: 0.8444 (mt) REVERT: A 280 LEU cc_start: 0.9105 (tp) cc_final: 0.8769 (tt) REVERT: A 722 LYS cc_start: 0.9138 (mttp) cc_final: 0.8825 (mmtm) REVERT: A 854 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8308 (t80) REVERT: A 915 TRP cc_start: 0.8069 (t-100) cc_final: 0.7631 (t-100) REVERT: A 1026 MET cc_start: 0.8694 (tpp) cc_final: 0.8471 (tpp) REVERT: A 1092 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8792 (t0) REVERT: A 1115 MET cc_start: 0.8182 (tpp) cc_final: 0.7913 (tpp) REVERT: A 1180 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8147 (tp30) REVERT: D 138 MET cc_start: 0.8902 (mmt) cc_final: 0.8463 (tpp) REVERT: D 465 ARG cc_start: 0.7125 (mmp-170) cc_final: 0.6638 (mmm160) REVERT: D 625 MET cc_start: 0.8432 (mtt) cc_final: 0.8183 (mtp) REVERT: D 983 MET cc_start: 0.8767 (mmm) cc_final: 0.8537 (mmm) REVERT: D 992 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9026 (mp) REVERT: D 1102 SER cc_start: 0.9035 (m) cc_final: 0.8614 (p) REVERT: D 1202 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 136 HIS cc_start: 0.8377 (m-70) cc_final: 0.8093 (m90) REVERT: B 457 MET cc_start: 0.8807 (tpt) cc_final: 0.8493 (tpt) REVERT: B 625 MET cc_start: 0.8979 (mmm) cc_final: 0.8495 (mmt) REVERT: B 682 LEU cc_start: 0.9601 (mt) cc_final: 0.9365 (mp) REVERT: B 895 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 935 MET cc_start: 0.8625 (tpp) cc_final: 0.8162 (tpp) REVERT: B 1081 ILE cc_start: 0.9281 (mm) cc_final: 0.9042 (mm) REVERT: B 1115 MET cc_start: 0.8207 (tpp) cc_final: 0.7874 (mpp) REVERT: B 1127 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8333 (tp) REVERT: B 1135 MET cc_start: 0.8170 (mtp) cc_final: 0.7932 (ptt) REVERT: B 1184 GLU cc_start: 0.8711 (tp30) cc_final: 0.8289 (tp30) outliers start: 54 outliers final: 32 residues processed: 494 average time/residue: 0.1786 time to fit residues: 148.7007 Evaluate side-chains 432 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 394 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1141 CYS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain D residue 1130 PHE Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1127 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 273 optimal weight: 0.0970 chunk 69 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 0.0970 chunk 108 optimal weight: 20.0000 chunk 132 optimal weight: 50.0000 chunk 398 optimal weight: 0.0970 chunk 380 optimal weight: 2.9990 overall best weight: 1.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 402 HIS A 475 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 637 HIS ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN D 867 ASN B 343 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.095369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.073718 restraints weight = 114722.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076247 restraints weight = 53893.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.077874 restraints weight = 32928.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.078956 restraints weight = 23743.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.079634 restraints weight = 19078.713| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33130 Z= 0.142 Angle : 0.617 8.522 45200 Z= 0.318 Chirality : 0.041 0.306 5279 Planarity : 0.005 0.080 5555 Dihedral : 8.049 59.933 6140 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 2.23 % Allowed : 9.52 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: -0.26 (0.13), residues: 4094 helix: 0.68 (0.10), residues: 2560 sheet: -1.07 (0.33), residues: 256 loop : -1.63 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 724 TYR 0.021 0.001 TYR C 549 PHE 0.023 0.001 PHE D 866 TRP 0.027 0.001 TRP D 915 HIS 0.013 0.001 HIS C 496 Details of bonding type rmsd covalent geometry : bond 0.00311 (33126) covalent geometry : angle 0.61658 (45192) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.60733 ( 8) hydrogen bonds : bond 0.04604 ( 1947) hydrogen bonds : angle 4.53538 ( 5757) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 419 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 429 LEU cc_start: 0.9105 (mt) cc_final: 0.8783 (pp) REVERT: C 442 PHE cc_start: 0.8751 (t80) cc_final: 0.8475 (m-10) REVERT: C 453 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7974 (tp) REVERT: C 566 PHE cc_start: 0.6594 (m-80) cc_final: 0.6082 (m-10) REVERT: C 722 LYS cc_start: 0.9163 (mttm) cc_final: 0.8895 (tptp) REVERT: C 724 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8096 (ttp80) REVERT: C 854 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8527 (t80) REVERT: C 1097 GLU cc_start: 0.8700 (pt0) cc_final: 0.8461 (pm20) REVERT: C 1179 GLU cc_start: 0.8459 (tt0) cc_final: 0.8090 (tp30) REVERT: C 1184 GLU cc_start: 0.8317 (tp30) cc_final: 0.7996 (tp30) REVERT: C 1187 ASP cc_start: 0.7712 (p0) cc_final: 0.7018 (p0) REVERT: A 121 MET cc_start: 0.8228 (mmm) cc_final: 0.7759 (tpp) REVERT: A 223 ILE cc_start: 0.8735 (tp) cc_final: 0.8517 (mt) REVERT: A 544 LEU cc_start: 0.8964 (mm) cc_final: 0.8661 (mm) REVERT: A 854 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8432 (t80) REVERT: A 915 TRP cc_start: 0.8105 (t-100) cc_final: 0.7674 (t-100) REVERT: A 979 MET cc_start: 0.8637 (mtp) cc_final: 0.8360 (ttm) REVERT: A 1115 MET cc_start: 0.8173 (tpp) cc_final: 0.7876 (tpp) REVERT: A 1132 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.6058 (t-170) REVERT: A 1180 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8159 (tp30) REVERT: D 138 MET cc_start: 0.8943 (mmt) cc_final: 0.8395 (tpt) REVERT: D 465 ARG cc_start: 0.7231 (mmp-170) cc_final: 0.6776 (mmm160) REVERT: D 625 MET cc_start: 0.8444 (mtt) cc_final: 0.8171 (mtp) REVERT: D 902 MET cc_start: 0.7623 (mmt) cc_final: 0.6682 (mtt) REVERT: D 978 MET cc_start: 0.8439 (mpp) cc_final: 0.7861 (mpp) REVERT: D 992 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9122 (mp) REVERT: D 1030 MET cc_start: 0.9362 (mtp) cc_final: 0.9098 (mtp) REVERT: D 1102 SER cc_start: 0.9040 (m) cc_final: 0.8521 (p) REVERT: D 1202 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 136 HIS cc_start: 0.8395 (m-70) cc_final: 0.8135 (m-70) REVERT: B 242 MET cc_start: 0.7777 (mmp) cc_final: 0.7545 (mmp) REVERT: B 457 MET cc_start: 0.8810 (tpt) cc_final: 0.8512 (tpt) REVERT: B 625 MET cc_start: 0.9064 (mmm) cc_final: 0.8697 (mmt) REVERT: B 895 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 1072 MET cc_start: 0.8709 (ttp) cc_final: 0.8415 (ttp) REVERT: B 1127 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8241 (tp) REVERT: B 1135 MET cc_start: 0.8187 (mtp) cc_final: 0.7956 (ptt) REVERT: B 1184 GLU cc_start: 0.8717 (tp30) cc_final: 0.8293 (tp30) outliers start: 70 outliers final: 47 residues processed: 466 average time/residue: 0.1697 time to fit residues: 134.6293 Evaluate side-chains 443 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 390 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 926 ILE Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain A residue 31 TRP Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 657 HIS Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain D residue 1130 PHE Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1134 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 143 optimal weight: 3.9990 chunk 390 optimal weight: 0.1980 chunk 180 optimal weight: 0.0980 chunk 20 optimal weight: 40.0000 chunk 199 optimal weight: 9.9990 chunk 314 optimal weight: 40.0000 chunk 370 optimal weight: 3.9990 chunk 388 optimal weight: 0.8980 chunk 361 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 HIS ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 HIS ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 657 HIS ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.095674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073876 restraints weight = 113935.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.076415 restraints weight = 53751.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078038 restraints weight = 32965.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079099 restraints weight = 23898.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079801 restraints weight = 19298.545| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33130 Z= 0.125 Angle : 0.581 9.400 45200 Z= 0.298 Chirality : 0.040 0.216 5279 Planarity : 0.004 0.074 5555 Dihedral : 7.620 59.882 6138 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 2.13 % Allowed : 11.05 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: 0.14 (0.13), residues: 4094 helix: 1.01 (0.10), residues: 2561 sheet: -0.93 (0.32), residues: 264 loop : -1.53 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 438 TYR 0.024 0.001 TYR D 543 PHE 0.021 0.001 PHE D1001 TRP 0.022 0.001 TRP C 142 HIS 0.022 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00271 (33126) covalent geometry : angle 0.58096 (45192) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.51875 ( 8) hydrogen bonds : bond 0.04239 ( 1947) hydrogen bonds : angle 4.31602 ( 5757) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 438 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TRP cc_start: 0.7107 (m-10) cc_final: 0.6847 (m-10) REVERT: C 303 ILE cc_start: 0.9192 (mp) cc_final: 0.8869 (tp) REVERT: C 429 LEU cc_start: 0.9148 (mt) cc_final: 0.8808 (pp) REVERT: C 442 PHE cc_start: 0.8712 (t80) cc_final: 0.8496 (m-10) REVERT: C 566 PHE cc_start: 0.6538 (m-80) cc_final: 0.5963 (m-10) REVERT: C 722 LYS cc_start: 0.9161 (mttm) cc_final: 0.8721 (tptt) REVERT: C 854 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8462 (t80) REVERT: C 1179 GLU cc_start: 0.8459 (tt0) cc_final: 0.8145 (tp30) REVERT: C 1184 GLU cc_start: 0.8309 (tp30) cc_final: 0.8011 (tp30) REVERT: C 1187 ASP cc_start: 0.7663 (p0) cc_final: 0.7065 (p0) REVERT: A 121 MET cc_start: 0.8269 (mmm) cc_final: 0.7812 (tpp) REVERT: A 223 ILE cc_start: 0.8750 (tp) cc_final: 0.8527 (mt) REVERT: A 386 MET cc_start: 0.7344 (tpp) cc_final: 0.6581 (tpp) REVERT: A 479 MET cc_start: 0.8892 (mmm) cc_final: 0.8473 (mmt) REVERT: A 544 LEU cc_start: 0.8936 (mm) cc_final: 0.8592 (mm) REVERT: A 854 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8519 (t80) REVERT: A 915 TRP cc_start: 0.8195 (t-100) cc_final: 0.7915 (t-100) REVERT: A 1026 MET cc_start: 0.8569 (tpp) cc_final: 0.8226 (tpp) REVERT: A 1115 MET cc_start: 0.8197 (tpp) cc_final: 0.7879 (tpp) REVERT: A 1132 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6234 (t-170) REVERT: A 1180 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8091 (tp30) REVERT: D 138 MET cc_start: 0.8947 (mmt) cc_final: 0.8402 (tpt) REVERT: D 465 ARG cc_start: 0.7247 (mmp-170) cc_final: 0.6873 (mmm160) REVERT: D 625 MET cc_start: 0.8416 (mtt) cc_final: 0.8114 (mtt) REVERT: D 902 MET cc_start: 0.7607 (mmt) cc_final: 0.6721 (mtt) REVERT: D 978 MET cc_start: 0.8429 (mpp) cc_final: 0.7820 (mpp) REVERT: D 992 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9149 (mp) REVERT: D 1032 TYR cc_start: 0.9091 (m-80) cc_final: 0.8742 (m-80) REVERT: D 1102 SER cc_start: 0.9033 (m) cc_final: 0.8524 (p) REVERT: D 1160 LEU cc_start: 0.9082 (tt) cc_final: 0.8836 (tt) REVERT: D 1202 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8054 (tm-30) REVERT: B 136 HIS cc_start: 0.8404 (m-70) cc_final: 0.8140 (m-70) REVERT: B 242 MET cc_start: 0.7887 (mmp) cc_final: 0.7680 (mmp) REVERT: B 429 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8726 (pp) REVERT: B 431 TRP cc_start: 0.8057 (m-10) cc_final: 0.7815 (m-10) REVERT: B 457 MET cc_start: 0.8767 (tpt) cc_final: 0.8493 (tpt) REVERT: B 625 MET cc_start: 0.9122 (mmm) cc_final: 0.8810 (mmt) REVERT: B 681 GLN cc_start: 0.8815 (tp40) cc_final: 0.8355 (tp40) REVERT: B 685 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 895 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 1127 LEU cc_start: 0.8860 (pt) cc_final: 0.8230 (tp) REVERT: B 1184 GLU cc_start: 0.8738 (tp30) cc_final: 0.8312 (tp30) REVERT: B 1207 MET cc_start: 0.8720 (mmt) cc_final: 0.8474 (mmp) outliers start: 67 outliers final: 48 residues processed: 477 average time/residue: 0.1731 time to fit residues: 139.7504 Evaluate side-chains 447 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 392 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1202 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 298 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1171 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B1080 ASN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.092509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069761 restraints weight = 116299.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072220 restraints weight = 55129.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.073817 restraints weight = 34221.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074846 restraints weight = 24950.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075519 restraints weight = 20356.539| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33130 Z= 0.221 Angle : 0.659 9.557 45200 Z= 0.336 Chirality : 0.042 0.212 5279 Planarity : 0.005 0.076 5555 Dihedral : 7.599 59.929 6134 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.24 % Rotamer: Outliers : 2.61 % Allowed : 12.54 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: 0.24 (0.13), residues: 4094 helix: 1.08 (0.10), residues: 2560 sheet: -0.91 (0.32), residues: 269 loop : -1.44 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 438 TYR 0.016 0.002 TYR D 952 PHE 0.023 0.002 PHE D 866 TRP 0.020 0.002 TRP D 621 HIS 0.015 0.001 HIS C 496 Details of bonding type rmsd covalent geometry : bond 0.00495 (33126) covalent geometry : angle 0.65882 (45192) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.67198 ( 8) hydrogen bonds : bond 0.04509 ( 1947) hydrogen bonds : angle 4.43971 ( 5757) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 394 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TRP cc_start: 0.7465 (m-10) cc_final: 0.7165 (m-10) REVERT: C 442 PHE cc_start: 0.8828 (t80) cc_final: 0.8358 (m-80) REVERT: C 483 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7881 (mm) REVERT: C 532 ILE cc_start: 0.7162 (mp) cc_final: 0.6859 (mt) REVERT: C 566 PHE cc_start: 0.6892 (m-80) cc_final: 0.6132 (m-10) REVERT: C 711 ASN cc_start: 0.9205 (m110) cc_final: 0.8882 (t0) REVERT: C 722 LYS cc_start: 0.9270 (mttm) cc_final: 0.8987 (tptp) REVERT: C 724 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8186 (ttp80) REVERT: C 854 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8464 (t80) REVERT: C 1179 GLU cc_start: 0.8511 (tt0) cc_final: 0.8204 (tp30) REVERT: C 1184 GLU cc_start: 0.8372 (tp30) cc_final: 0.8088 (tp30) REVERT: C 1187 ASP cc_start: 0.7618 (p0) cc_final: 0.7004 (p0) REVERT: A 121 MET cc_start: 0.8249 (mmm) cc_final: 0.7744 (tpp) REVERT: A 280 LEU cc_start: 0.9094 (tp) cc_final: 0.8768 (tt) REVERT: A 544 LEU cc_start: 0.9008 (mm) cc_final: 0.8665 (mm) REVERT: A 854 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8452 (t80) REVERT: A 915 TRP cc_start: 0.8345 (t-100) cc_final: 0.7906 (t-100) REVERT: A 1026 MET cc_start: 0.8614 (tpp) cc_final: 0.8397 (tpp) REVERT: A 1115 MET cc_start: 0.8177 (tpp) cc_final: 0.7871 (tpp) REVERT: A 1132 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6266 (t-170) REVERT: A 1180 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7886 (tp30) REVERT: D 138 MET cc_start: 0.8955 (mmt) cc_final: 0.8441 (tpt) REVERT: D 625 MET cc_start: 0.8432 (mtt) cc_final: 0.8225 (mtt) REVERT: D 671 GLU cc_start: 0.8005 (tp30) cc_final: 0.7746 (tp30) REVERT: D 902 MET cc_start: 0.7605 (mmt) cc_final: 0.6841 (mtt) REVERT: D 978 MET cc_start: 0.8427 (mpp) cc_final: 0.7847 (mpp) REVERT: D 992 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9253 (mp) REVERT: D 1102 SER cc_start: 0.9081 (m) cc_final: 0.8627 (p) REVERT: D 1202 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 136 HIS cc_start: 0.8526 (m-70) cc_final: 0.8275 (m-70) REVERT: B 242 MET cc_start: 0.7978 (mmp) cc_final: 0.7766 (mmp) REVERT: B 429 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8975 (mm) REVERT: B 431 TRP cc_start: 0.8141 (m-10) cc_final: 0.7883 (m-10) REVERT: B 457 MET cc_start: 0.8821 (tpt) cc_final: 0.8548 (tpt) REVERT: B 544 LEU cc_start: 0.8782 (mm) cc_final: 0.8346 (mm) REVERT: B 625 MET cc_start: 0.9217 (mmm) cc_final: 0.8894 (mmt) REVERT: B 1115 MET cc_start: 0.8158 (tpp) cc_final: 0.7865 (mpp) REVERT: B 1127 LEU cc_start: 0.8943 (pt) cc_final: 0.8270 (tp) REVERT: B 1184 GLU cc_start: 0.8656 (tp30) cc_final: 0.8277 (tp30) outliers start: 82 outliers final: 55 residues processed: 453 average time/residue: 0.1695 time to fit residues: 130.3417 Evaluate side-chains 434 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 373 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 926 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1141 CYS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain D residue 1130 PHE Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1202 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 69 optimal weight: 3.9990 chunk 350 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 252 optimal weight: 7.9990 chunk 286 optimal weight: 8.9990 chunk 309 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 280 optimal weight: 7.9990 chunk 327 optimal weight: 0.0570 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 942 GLN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.094528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.072257 restraints weight = 114919.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074987 restraints weight = 58593.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.077104 restraints weight = 32913.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.077224 restraints weight = 23686.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077234 restraints weight = 21896.252| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33130 Z= 0.128 Angle : 0.601 11.239 45200 Z= 0.303 Chirality : 0.040 0.340 5279 Planarity : 0.004 0.073 5555 Dihedral : 7.252 59.968 6134 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 2.20 % Allowed : 13.82 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: 0.46 (0.13), residues: 4094 helix: 1.24 (0.10), residues: 2569 sheet: -0.77 (0.32), residues: 271 loop : -1.39 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 465 TYR 0.015 0.001 TYR D 691 PHE 0.038 0.001 PHE D 866 TRP 0.021 0.001 TRP D 621 HIS 0.006 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00278 (33126) covalent geometry : angle 0.60087 (45192) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.50569 ( 8) hydrogen bonds : bond 0.04147 ( 1947) hydrogen bonds : angle 4.22793 ( 5757) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 415 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TRP cc_start: 0.7529 (m-10) cc_final: 0.7281 (m-10) REVERT: C 442 PHE cc_start: 0.8777 (t80) cc_final: 0.8351 (m-80) REVERT: C 483 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8160 (mm) REVERT: C 532 ILE cc_start: 0.7126 (mp) cc_final: 0.6832 (mt) REVERT: C 566 PHE cc_start: 0.6864 (m-80) cc_final: 0.6097 (m-10) REVERT: C 722 LYS cc_start: 0.9185 (mttm) cc_final: 0.8807 (tptt) REVERT: C 724 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7750 (ttp80) REVERT: C 854 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8403 (t80) REVERT: C 1179 GLU cc_start: 0.8447 (tt0) cc_final: 0.8156 (tp30) REVERT: C 1184 GLU cc_start: 0.8349 (tp30) cc_final: 0.8115 (tp30) REVERT: C 1187 ASP cc_start: 0.7694 (p0) cc_final: 0.7300 (p0) REVERT: A 121 MET cc_start: 0.8258 (mmm) cc_final: 0.7721 (tpp) REVERT: A 280 LEU cc_start: 0.9111 (tp) cc_final: 0.8786 (tt) REVERT: A 544 LEU cc_start: 0.8966 (mm) cc_final: 0.8616 (mm) REVERT: A 722 LYS cc_start: 0.9170 (mttp) cc_final: 0.8958 (mtpt) REVERT: A 854 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8563 (t80) REVERT: A 915 TRP cc_start: 0.8291 (t-100) cc_final: 0.7984 (t-100) REVERT: A 1115 MET cc_start: 0.8183 (tpp) cc_final: 0.7928 (tpp) REVERT: A 1132 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6209 (t-170) REVERT: D 138 MET cc_start: 0.9012 (mmt) cc_final: 0.8423 (tpt) REVERT: D 397 MET cc_start: 0.7965 (tpp) cc_final: 0.7718 (tpp) REVERT: D 465 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7423 (mmm-85) REVERT: D 902 MET cc_start: 0.7585 (mmt) cc_final: 0.6782 (mtt) REVERT: D 978 MET cc_start: 0.8384 (mpp) cc_final: 0.7756 (mpp) REVERT: D 992 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9229 (mp) REVERT: D 1102 SER cc_start: 0.9020 (m) cc_final: 0.8570 (p) REVERT: D 1202 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 136 HIS cc_start: 0.8645 (m-70) cc_final: 0.8373 (m-70) REVERT: B 242 MET cc_start: 0.8015 (mmp) cc_final: 0.7743 (mmp) REVERT: B 337 ASP cc_start: 0.8412 (m-30) cc_final: 0.8071 (m-30) REVERT: B 429 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8705 (pp) REVERT: B 431 TRP cc_start: 0.8089 (m-10) cc_final: 0.7859 (m-10) REVERT: B 457 MET cc_start: 0.8792 (tpt) cc_final: 0.8566 (tpt) REVERT: B 625 MET cc_start: 0.9183 (mmm) cc_final: 0.8864 (mmt) REVERT: B 1127 LEU cc_start: 0.8919 (pt) cc_final: 0.8282 (tp) REVERT: B 1184 GLU cc_start: 0.8548 (tp30) cc_final: 0.8234 (tp30) outliers start: 69 outliers final: 54 residues processed: 465 average time/residue: 0.1714 time to fit residues: 135.3001 Evaluate side-chains 445 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 385 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1141 CYS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 681 GLN Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 890 PHE Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain D residue 1130 PHE Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1202 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 286 optimal weight: 7.9990 chunk 407 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 356 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 217 optimal weight: 0.4980 chunk 20 optimal weight: 50.0000 chunk 31 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 446 GLN C1080 ASN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN D 283 HIS ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.090856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068125 restraints weight = 117339.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070511 restraints weight = 56224.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072059 restraints weight = 35054.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073072 restraints weight = 25708.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073733 restraints weight = 21002.953| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 33130 Z= 0.272 Angle : 0.734 12.575 45200 Z= 0.369 Chirality : 0.044 0.310 5279 Planarity : 0.005 0.078 5555 Dihedral : 7.525 59.584 6134 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 2.80 % Allowed : 13.72 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: 0.24 (0.13), residues: 4094 helix: 1.05 (0.10), residues: 2560 sheet: -0.90 (0.32), residues: 270 loop : -1.37 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 465 TYR 0.017 0.002 TYR D 952 PHE 0.031 0.002 PHE A 866 TRP 0.028 0.002 TRP D 621 HIS 0.007 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00607 (33126) covalent geometry : angle 0.73393 (45192) SS BOND : bond 0.00732 ( 4) SS BOND : angle 1.28466 ( 8) hydrogen bonds : bond 0.04681 ( 1947) hydrogen bonds : angle 4.55345 ( 5757) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 374 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TRP cc_start: 0.7722 (m-10) cc_final: 0.7449 (m-10) REVERT: C 446 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: C 483 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7917 (mm) REVERT: C 532 ILE cc_start: 0.7240 (mp) cc_final: 0.6941 (mt) REVERT: C 854 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8411 (t80) REVERT: C 1097 GLU cc_start: 0.8760 (pt0) cc_final: 0.8443 (pm20) REVERT: C 1179 GLU cc_start: 0.8491 (tt0) cc_final: 0.8233 (tp30) REVERT: C 1221 MET cc_start: 0.8128 (mmm) cc_final: 0.7548 (mmt) REVERT: A 121 MET cc_start: 0.8318 (mmm) cc_final: 0.7777 (tpp) REVERT: A 280 LEU cc_start: 0.9106 (tp) cc_final: 0.8759 (tt) REVERT: A 544 LEU cc_start: 0.9023 (mm) cc_final: 0.8697 (mm) REVERT: A 722 LYS cc_start: 0.9229 (mttp) cc_final: 0.9025 (mtpt) REVERT: A 854 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8440 (t80) REVERT: A 1026 MET cc_start: 0.8652 (tpp) cc_final: 0.8443 (tpp) REVERT: A 1115 MET cc_start: 0.8160 (tpp) cc_final: 0.7874 (tpp) REVERT: A 1132 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.6078 (t-170) REVERT: D 138 MET cc_start: 0.8979 (mmt) cc_final: 0.8445 (tpt) REVERT: D 397 MET cc_start: 0.7857 (tpp) cc_final: 0.7647 (tpp) REVERT: D 465 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7507 (mmm-85) REVERT: D 619 MET cc_start: 0.9161 (tpp) cc_final: 0.8750 (ttm) REVERT: D 902 MET cc_start: 0.7677 (mmt) cc_final: 0.6958 (mtt) REVERT: D 978 MET cc_start: 0.8432 (mpp) cc_final: 0.7814 (mpp) REVERT: D 992 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9285 (mp) REVERT: D 1102 SER cc_start: 0.9080 (m) cc_final: 0.8643 (p) REVERT: D 1202 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8053 (tm-30) REVERT: B 136 HIS cc_start: 0.8602 (m-70) cc_final: 0.8346 (m-70) REVERT: B 457 MET cc_start: 0.8814 (tpt) cc_final: 0.8601 (tpt) REVERT: B 544 LEU cc_start: 0.8808 (mm) cc_final: 0.8395 (mm) REVERT: B 625 MET cc_start: 0.9304 (mmm) cc_final: 0.8987 (mmt) REVERT: B 1086 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8960 (mp) REVERT: B 1115 MET cc_start: 0.8113 (mpp) cc_final: 0.7902 (mpp) REVERT: B 1184 GLU cc_start: 0.8600 (tp30) cc_final: 0.8294 (tp30) outliers start: 88 outliers final: 62 residues processed: 446 average time/residue: 0.1826 time to fit residues: 138.3068 Evaluate side-chains 432 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 363 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 446 GLN Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 926 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1127 LEU Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1141 CYS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain D residue 1130 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1211 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 321 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 132 optimal weight: 50.0000 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 301 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 359 optimal weight: 0.4980 chunk 380 optimal weight: 4.9990 chunk 316 optimal weight: 0.9990 overall best weight: 0.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 HIS A 917 GLN A1093 ASN ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.094122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071747 restraints weight = 115290.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074255 restraints weight = 55348.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.075832 restraints weight = 34274.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.076882 restraints weight = 25041.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.077448 restraints weight = 20356.938| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33130 Z= 0.124 Angle : 0.627 13.017 45200 Z= 0.312 Chirality : 0.041 0.394 5279 Planarity : 0.004 0.075 5555 Dihedral : 6.977 59.544 6132 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.23 % Allowed : 14.52 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: 0.54 (0.13), residues: 4094 helix: 1.30 (0.10), residues: 2565 sheet: -0.78 (0.32), residues: 267 loop : -1.31 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 438 TYR 0.017 0.001 TYR B 862 PHE 0.020 0.001 PHE D 866 TRP 0.035 0.002 TRP B 431 HIS 0.006 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00264 (33126) covalent geometry : angle 0.62715 (45192) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.57434 ( 8) hydrogen bonds : bond 0.04144 ( 1947) hydrogen bonds : angle 4.23024 ( 5757) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 413 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 286 LEU cc_start: 0.9185 (mm) cc_final: 0.8829 (pp) REVERT: C 438 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8472 (ttm-80) REVERT: C 442 PHE cc_start: 0.8813 (t80) cc_final: 0.8472 (m-80) REVERT: C 483 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8026 (mm) REVERT: C 532 ILE cc_start: 0.7247 (mp) cc_final: 0.6939 (mt) REVERT: C 566 PHE cc_start: 0.6689 (m-80) cc_final: 0.5768 (m-10) REVERT: C 711 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8633 (t0) REVERT: C 854 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8349 (t80) REVERT: C 978 MET cc_start: 0.8309 (mmm) cc_final: 0.8077 (mpp) REVERT: C 1097 GLU cc_start: 0.8756 (pt0) cc_final: 0.8549 (pm20) REVERT: C 1179 GLU cc_start: 0.8455 (tt0) cc_final: 0.8169 (tp30) REVERT: C 1187 ASP cc_start: 0.7653 (p0) cc_final: 0.7388 (p0) REVERT: A 121 MET cc_start: 0.8265 (mmm) cc_final: 0.7757 (tpp) REVERT: A 544 LEU cc_start: 0.8999 (mm) cc_final: 0.8630 (mm) REVERT: A 722 LYS cc_start: 0.9185 (mttp) cc_final: 0.8802 (mtpp) REVERT: A 854 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8546 (t80) REVERT: A 1026 MET cc_start: 0.8531 (tpp) cc_final: 0.8061 (tpp) REVERT: A 1115 MET cc_start: 0.8155 (tpp) cc_final: 0.7883 (tpp) REVERT: A 1132 HIS cc_start: 0.6984 (OUTLIER) cc_final: 0.6073 (t-170) REVERT: D 138 MET cc_start: 0.8964 (mmt) cc_final: 0.8402 (tpt) REVERT: D 457 MET cc_start: 0.8376 (mmt) cc_final: 0.8072 (mmm) REVERT: D 465 ARG cc_start: 0.7919 (mmt180) cc_final: 0.7568 (mmm-85) REVERT: D 619 MET cc_start: 0.9174 (tpp) cc_final: 0.8901 (tpp) REVERT: D 902 MET cc_start: 0.7567 (mmt) cc_final: 0.6918 (mtt) REVERT: D 978 MET cc_start: 0.8442 (mpp) cc_final: 0.7836 (mpp) REVERT: D 992 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9237 (mp) REVERT: D 1102 SER cc_start: 0.9013 (m) cc_final: 0.8597 (p) REVERT: D 1202 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7884 (tm-30) REVERT: B 136 HIS cc_start: 0.8579 (m-70) cc_final: 0.8305 (m-70) REVERT: B 242 MET cc_start: 0.7349 (mmp) cc_final: 0.7147 (tmm) REVERT: B 337 ASP cc_start: 0.8474 (m-30) cc_final: 0.8146 (m-30) REVERT: B 457 MET cc_start: 0.8754 (tpt) cc_final: 0.8542 (tpt) REVERT: B 544 LEU cc_start: 0.8754 (mm) cc_final: 0.8325 (mm) REVERT: B 625 MET cc_start: 0.9256 (mmm) cc_final: 0.8976 (mmt) REVERT: B 1086 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8886 (mp) outliers start: 70 outliers final: 48 residues processed: 465 average time/residue: 0.1820 time to fit residues: 145.1465 Evaluate side-chains 440 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 385 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain D residue 1130 PHE Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1134 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 391 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 335 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 354 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 chunk 372 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN C 711 ASN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.092191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069561 restraints weight = 115937.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071987 restraints weight = 55345.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073572 restraints weight = 34425.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074607 restraints weight = 25110.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.075289 restraints weight = 20454.531| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33130 Z= 0.200 Angle : 0.684 11.739 45200 Z= 0.340 Chirality : 0.043 0.352 5279 Planarity : 0.005 0.073 5555 Dihedral : 7.069 59.702 6132 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 2.39 % Allowed : 15.12 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: 0.53 (0.13), residues: 4094 helix: 1.28 (0.10), residues: 2566 sheet: -0.85 (0.32), residues: 266 loop : -1.27 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 724 TYR 0.017 0.001 TYR B 862 PHE 0.020 0.002 PHE D 866 TRP 0.076 0.002 TRP A 915 HIS 0.007 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00448 (33126) covalent geometry : angle 0.68407 (45192) SS BOND : bond 0.00462 ( 4) SS BOND : angle 0.78363 ( 8) hydrogen bonds : bond 0.04321 ( 1947) hydrogen bonds : angle 4.37156 ( 5757) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 381 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 TRP cc_start: 0.7616 (m100) cc_final: 0.7145 (m100) REVERT: C 438 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8474 (ttm-80) REVERT: C 442 PHE cc_start: 0.8863 (t80) cc_final: 0.8364 (m-80) REVERT: C 483 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7999 (mm) REVERT: C 566 PHE cc_start: 0.6775 (m-80) cc_final: 0.5829 (m-10) REVERT: C 711 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.8858 (t0) REVERT: C 854 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8366 (t80) REVERT: C 1097 GLU cc_start: 0.8772 (pt0) cc_final: 0.8547 (pm20) REVERT: C 1179 GLU cc_start: 0.8461 (tt0) cc_final: 0.8200 (tp30) REVERT: A 121 MET cc_start: 0.8263 (mmm) cc_final: 0.7748 (tpp) REVERT: A 280 LEU cc_start: 0.9098 (tp) cc_final: 0.8806 (tt) REVERT: A 544 LEU cc_start: 0.8953 (mm) cc_final: 0.8577 (mm) REVERT: A 722 LYS cc_start: 0.9201 (mttp) cc_final: 0.8997 (mtpt) REVERT: A 854 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8517 (t80) REVERT: A 984 MET cc_start: 0.8641 (mmm) cc_final: 0.8428 (mmm) REVERT: A 1026 MET cc_start: 0.8588 (tpp) cc_final: 0.8360 (tpp) REVERT: A 1093 ASN cc_start: 0.8340 (m-40) cc_final: 0.8096 (m-40) REVERT: A 1115 MET cc_start: 0.8114 (tpp) cc_final: 0.7861 (tpp) REVERT: A 1132 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6124 (t-170) REVERT: A 1180 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8220 (mt-10) REVERT: D 138 MET cc_start: 0.8945 (mmt) cc_final: 0.8398 (tpt) REVERT: D 465 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7556 (mmm-85) REVERT: D 655 MET cc_start: 0.8758 (mtm) cc_final: 0.8556 (mtt) REVERT: D 902 MET cc_start: 0.7593 (mmt) cc_final: 0.6981 (mtt) REVERT: D 978 MET cc_start: 0.8409 (mpp) cc_final: 0.7787 (mpp) REVERT: D 992 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9271 (mp) REVERT: D 1102 SER cc_start: 0.9041 (m) cc_final: 0.8609 (p) REVERT: D 1202 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 136 HIS cc_start: 0.8569 (m-70) cc_final: 0.8307 (m-70) REVERT: B 242 MET cc_start: 0.7423 (mmp) cc_final: 0.7066 (tmm) REVERT: B 457 MET cc_start: 0.8759 (tpt) cc_final: 0.8537 (tpt) REVERT: B 544 LEU cc_start: 0.8780 (mm) cc_final: 0.8321 (mm) REVERT: B 1086 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8895 (mp) outliers start: 75 outliers final: 59 residues processed: 439 average time/residue: 0.1818 time to fit residues: 137.6749 Evaluate side-chains 439 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 373 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain D residue 1130 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 340 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 364 optimal weight: 0.4980 chunk 183 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 228 optimal weight: 6.9990 chunk 84 optimal weight: 0.0980 chunk 198 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.094466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.072275 restraints weight = 114999.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.074758 restraints weight = 55355.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076341 restraints weight = 34395.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077402 restraints weight = 25058.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.078109 restraints weight = 20292.058| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33130 Z= 0.123 Angle : 0.653 13.420 45200 Z= 0.319 Chirality : 0.041 0.377 5279 Planarity : 0.004 0.069 5555 Dihedral : 6.745 59.995 6132 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 2.04 % Allowed : 15.79 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: 0.66 (0.13), residues: 4094 helix: 1.39 (0.10), residues: 2567 sheet: -0.68 (0.32), residues: 267 loop : -1.25 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 724 TYR 0.018 0.001 TYR B 862 PHE 0.017 0.001 PHE D 866 TRP 0.063 0.002 TRP A 915 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00261 (33126) covalent geometry : angle 0.65285 (45192) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.53343 ( 8) hydrogen bonds : bond 0.04038 ( 1947) hydrogen bonds : angle 4.18645 ( 5757) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 408 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 TRP cc_start: 0.7531 (m100) cc_final: 0.7101 (m100) REVERT: C 438 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8459 (ttm-80) REVERT: C 442 PHE cc_start: 0.8795 (t80) cc_final: 0.8380 (m-80) REVERT: C 483 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8090 (mm) REVERT: C 532 ILE cc_start: 0.7190 (mp) cc_final: 0.6842 (mt) REVERT: C 566 PHE cc_start: 0.6564 (m-80) cc_final: 0.5622 (m-10) REVERT: C 711 ASN cc_start: 0.9236 (m-40) cc_final: 0.8996 (t0) REVERT: C 854 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8315 (t80) REVERT: C 1179 GLU cc_start: 0.8442 (tt0) cc_final: 0.8152 (tp30) REVERT: A 121 MET cc_start: 0.8278 (mmm) cc_final: 0.7768 (tpp) REVERT: A 479 MET cc_start: 0.8804 (mmm) cc_final: 0.8362 (mmt) REVERT: A 544 LEU cc_start: 0.8963 (mm) cc_final: 0.8578 (mm) REVERT: A 722 LYS cc_start: 0.9191 (mttp) cc_final: 0.8833 (mtpp) REVERT: A 854 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8518 (t80) REVERT: A 1026 MET cc_start: 0.8532 (tpp) cc_final: 0.8077 (tpp) REVERT: A 1093 ASN cc_start: 0.8311 (m-40) cc_final: 0.8087 (m-40) REVERT: A 1115 MET cc_start: 0.8156 (tpp) cc_final: 0.7879 (tpp) REVERT: A 1132 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6113 (t-170) REVERT: A 1180 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 138 MET cc_start: 0.8979 (mmt) cc_final: 0.8410 (tpt) REVERT: D 465 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7528 (mmm-85) REVERT: D 655 MET cc_start: 0.8727 (mtm) cc_final: 0.8516 (mtt) REVERT: D 902 MET cc_start: 0.7550 (mmt) cc_final: 0.6932 (mtt) REVERT: D 932 SER cc_start: 0.8910 (m) cc_final: 0.8612 (p) REVERT: D 978 MET cc_start: 0.8457 (mpp) cc_final: 0.7833 (mpp) REVERT: D 992 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9191 (mp) REVERT: D 994 MET cc_start: 0.8943 (tpp) cc_final: 0.8696 (tpt) REVERT: D 1030 MET cc_start: 0.9252 (mtp) cc_final: 0.8994 (mtp) REVERT: D 1102 SER cc_start: 0.8977 (m) cc_final: 0.8561 (p) REVERT: D 1202 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7820 (tm-30) REVERT: B 136 HIS cc_start: 0.8563 (m-70) cc_final: 0.8289 (m-70) REVERT: B 242 MET cc_start: 0.7374 (mmp) cc_final: 0.7109 (tmm) REVERT: B 337 ASP cc_start: 0.8453 (m-30) cc_final: 0.8121 (m-30) REVERT: B 431 TRP cc_start: 0.8113 (m-90) cc_final: 0.7866 (m-90) REVERT: B 457 MET cc_start: 0.8732 (tpt) cc_final: 0.8528 (tpt) outliers start: 64 outliers final: 51 residues processed: 455 average time/residue: 0.1808 time to fit residues: 141.5863 Evaluate side-chains 442 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 386 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 1219 HIS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1128 ILE Chi-restraints excluded: chain D residue 1130 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 367 optimal weight: 4.9990 chunk 150 optimal weight: 0.0050 chunk 106 optimal weight: 40.0000 chunk 183 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 315 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.092078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069493 restraints weight = 116476.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071932 restraints weight = 55706.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.073494 restraints weight = 34697.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.074516 restraints weight = 25388.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.075016 restraints weight = 20712.739| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 33130 Z= 0.208 Angle : 0.702 15.790 45200 Z= 0.348 Chirality : 0.044 0.359 5279 Planarity : 0.005 0.072 5555 Dihedral : 6.944 59.942 6132 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 2.10 % Allowed : 15.70 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % 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 are not related in a simple way. whole: 0.61 (0.13), residues: 4094 helix: 1.33 (0.10), residues: 2564 sheet: -0.78 (0.32), residues: 270 loop : -1.19 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 724 TYR 0.022 0.002 TYR B 862 PHE 0.021 0.002 PHE D 866 TRP 0.056 0.002 TRP A 915 HIS 0.007 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00468 (33126) covalent geometry : angle 0.70214 (45192) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.71285 ( 8) hydrogen bonds : bond 0.04301 ( 1947) hydrogen bonds : angle 4.36702 ( 5757) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5762.38 seconds wall clock time: 100 minutes 43.20 seconds (6043.20 seconds total)