Starting phenix.real_space_refine on Sat Mar 7 01:21:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v3l_31683/03_2026/7v3l_31683_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v3l_31683/03_2026/7v3l_31683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v3l_31683/03_2026/7v3l_31683_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v3l_31683/03_2026/7v3l_31683_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v3l_31683/03_2026/7v3l_31683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v3l_31683/03_2026/7v3l_31683.map" } resolution = 3.47 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= 0.002 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 195 5.16 5 C 22952 2.51 5 N 6002 2.21 5 O 7089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36238 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1131, 8731 Classifications: {'peptide': 1131} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 1080} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 1131, 8731 Classifications: {'peptide': 1131} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 1080} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 8918 Chain: "B" Number of atoms: 8785 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1135, 8779 Classifications: {'peptide': 1135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1084} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 1135, 8779 Classifications: {'peptide': 1135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1084} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 8968 Chain: "C" Number of atoms: 8719 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1126, 8713 Classifications: {'peptide': 1126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 49, 'TRANS': 1076} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 1126, 8713 Classifications: {'peptide': 1126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 49, 'TRANS': 1076} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 8899 Chain: "D" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1688 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "E" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1688 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "G" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "H" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1681 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1638 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER A 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER A 51 " occ=0.54 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 13.66, per 1000 atoms: 0.38 Number of scatterers: 36238 At special positions: 0 Unit cell: (199.801, 234.176, 226.656, 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 195 16.00 O 7089 8.00 N 6002 7.00 C 22952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.02 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.04 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.05 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.02 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.05 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.02 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.06 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.05 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.06 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.02 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.05 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.05 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.06 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 91 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.04 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.04 Simple disulfide: pdb=" SG CYS F 158 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 26 " - pdb=" SG CYS G 91 " distance=2.04 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 198 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS H 158 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 198 " 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: 3.69 Conformation dependent library (CDL) restraints added in 2.8 seconds 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8766 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 85 sheets defined 19.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.020A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.535A pdb=" N GLN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.733A pdb=" N GLN A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.957A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.847A pdb=" N TYR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.948A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.554A pdb=" N GLN A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.594A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.526A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 987 through 993 removed outlier: 3.615A pdb=" N ASN A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 Processing helix chain 'A' and resid 1013 through 1016 Processing helix chain 'A' and resid 1017 through 1043 removed outlier: 4.241A pdb=" N THR A1043 " --> pdb=" O GLU A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1106 Processing helix chain 'A' and resid 1114 through 1118 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.747A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.328A pdb=" N SER B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.857A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.668A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.733A pdb=" N GLN B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.957A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 825 through 852 removed outlier: 3.715A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.739A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 Processing helix chain 'B' and resid 987 through 995 removed outlier: 3.530A pdb=" N SER B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN B 994 " --> pdb=" O LEU B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1011 removed outlier: 3.505A pdb=" N GLY B1011 " --> pdb=" O ALA B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1041 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.825A pdb=" N ALA B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B1073 " --> pdb=" O ARG B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1177 removed outlier: 3.990A pdb=" N ASN B1176 " --> pdb=" O ILE B1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.945A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.733A pdb=" N GLN C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.957A pdb=" N SER C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 825 through 852 removed outlier: 3.780A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 925 through 930 removed outlier: 3.789A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 959 removed outlier: 4.906A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 Processing helix chain 'C' and resid 987 through 993 Processing helix chain 'C' and resid 997 through 1011 Processing helix chain 'C' and resid 1016 through 1035 removed outlier: 3.541A pdb=" N GLN C1020 " --> pdb=" O ASN C1016 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1040 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 4.238A pdb=" N ALA C1065 " --> pdb=" O LEU C1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 203 through 210 removed outlier: 3.560A pdb=" N GLY D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 203 through 210 removed outlier: 3.560A pdb=" N GLY F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 132 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 174 through 176 No H-bonds generated for 'chain 'H' and resid 174 through 176' Processing helix chain 'H' and resid 203 through 210 Processing helix chain 'I' and resid 125 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 7.696A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 75 removed outlier: 4.431A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 4.089A pdb=" N ALA A 282 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.741A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.741A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 182 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA8, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.207A pdb=" N HIS A 208 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 366 removed outlier: 4.671A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 662 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 671 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 405 removed outlier: 3.700A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 569 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 482 " --> pdb=" O MET A 569 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 477 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 498 through 499 removed outlier: 4.384A pdb=" N LEU A 554 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 506 removed outlier: 3.831A pdb=" N VAL A 514 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 605 through 607 removed outlier: 3.618A pdb=" N TYR A 606 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 779 through 782 Processing sheet with id=AB7, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.656A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 967 through 968 removed outlier: 3.989A pdb=" N PHE A 967 " --> pdb=" O SER C 781 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1122 through 1124 removed outlier: 3.888A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1127 through 1130 Processing sheet with id=AC2, first strand: chain 'A' and resid 1155 through 1156 Processing sheet with id=AC3, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.435A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.589A pdb=" N GLU B 252 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 282 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.555A pdb=" N ILE B 300 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.730A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 293 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET B 148 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.730A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 293 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET B 148 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 182 " --> pdb=" O TYR B 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.723A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AD2, first strand: chain 'B' and resid 360 through 367 removed outlier: 5.365A pdb=" N SER B 362 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 661 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER B 364 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 659 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 400 through 405 removed outlier: 3.700A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 569 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 482 " --> pdb=" O MET B 569 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 477 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 498 through 499 removed outlier: 4.384A pdb=" N LEU B 554 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 504 through 506 removed outlier: 3.831A pdb=" N VAL B 514 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 606 through 607 removed outlier: 3.595A pdb=" N GLY B 613 " --> pdb=" O TYR B 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 617 through 619 Processing sheet with id=AD8, first strand: chain 'B' and resid 778 through 783 removed outlier: 3.649A pdb=" N PHE B 778 " --> pdb=" O SER B1151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 793 through 794 removed outlier: 3.514A pdb=" N PHE B1126 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AE2, first strand: chain 'B' and resid 1155 through 1156 Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.855A pdb=" N VAL C 102 " --> pdb=" O ASP C 34 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.402A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.532A pdb=" N TYR C 292 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 150 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 235 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 279 through 284 removed outlier: 5.606A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 120 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.684A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE9, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AF1, first strand: chain 'C' and resid 366 through 367 Processing sheet with id=AF2, first strand: chain 'C' and resid 400 through 405 removed outlier: 3.700A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 477 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 422 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 498 through 499 removed outlier: 4.384A pdb=" N LEU C 554 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 504 through 506 removed outlier: 3.831A pdb=" N VAL C 514 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 605 through 607 Processing sheet with id=AF6, first strand: chain 'C' and resid 1122 through 1124 Processing sheet with id=AF7, first strand: chain 'C' and resid 1127 through 1130 Processing sheet with id=AF8, first strand: chain 'D' and resid 6 through 9 Processing sheet with id=AF9, first strand: chain 'D' and resid 14 through 15 removed outlier: 4.081A pdb=" N GLY D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 138 through 141 removed outlier: 4.694A pdb=" N ASP D 162 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR D 194 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 168 through 172 removed outlier: 3.528A pdb=" N HIS D 218 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 223 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AG4, first strand: chain 'E' and resid 14 through 15 removed outlier: 6.386A pdb=" N LEU E 14 " --> pdb=" O GLU E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AG6, first strand: chain 'E' and resid 47 through 49 removed outlier: 3.628A pdb=" N GLN E 93 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR E 101 " --> pdb=" O GLN E 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=AG8, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.752A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.682A pdb=" N TRP E 152 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 200 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL E 209 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 6 through 9 Processing sheet with id=AH2, first strand: chain 'F' and resid 14 through 15 removed outlier: 4.081A pdb=" N GLY F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 138 through 141 removed outlier: 4.694A pdb=" N ASP F 162 " --> pdb=" O TYR F 194 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR F 194 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU F 193 " --> pdb=" O GLN F 189 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 168 through 172 removed outlier: 3.528A pdb=" N HIS F 218 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR F 223 " --> pdb=" O HIS F 218 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 7 through 8 Processing sheet with id=AH6, first strand: chain 'G' and resid 14 through 15 removed outlier: 6.386A pdb=" N LEU G 14 " --> pdb=" O GLU G 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'G' and resid 22 through 24 Processing sheet with id=AH8, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.628A pdb=" N GLN G 93 " --> pdb=" O THR G 101 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR G 101 " --> pdb=" O GLN G 93 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AI1, first strand: chain 'G' and resid 118 through 122 removed outlier: 5.752A pdb=" N TYR G 177 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 157 through 159 removed outlier: 4.682A pdb=" N TRP G 152 " --> pdb=" O GLN G 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS G 149 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL G 200 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL G 209 " --> pdb=" O VAL G 200 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 6 through 9 Processing sheet with id=AI4, first strand: chain 'H' and resid 14 through 15 removed outlier: 4.082A pdb=" N GLY H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 138 through 141 removed outlier: 3.670A pdb=" N LEU H 196 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 169 through 172 removed outlier: 3.714A pdb=" N HIS H 218 " --> pdb=" O THR H 223 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR H 223 " --> pdb=" O HIS H 218 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 7 through 8 Processing sheet with id=AI8, first strand: chain 'I' and resid 14 through 15 removed outlier: 6.386A pdb=" N LEU I 14 " --> pdb=" O GLU I 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'I' and resid 22 through 24 Processing sheet with id=AJ1, first strand: chain 'I' and resid 47 through 49 Processing sheet with id=AJ2, first strand: chain 'I' and resid 51 through 52 Processing sheet with id=AJ3, first strand: chain 'I' and resid 118 through 122 removed outlier: 5.751A pdb=" N TYR I 177 " --> pdb=" O ASN I 142 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'I' and resid 157 through 159 removed outlier: 4.682A pdb=" N TRP I 152 " --> pdb=" O GLN I 159 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS I 149 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL I 200 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL I 209 " --> pdb=" O VAL I 200 " (cutoff:3.500A) 1233 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.01 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5964 1.31 - 1.44: 10400 1.44 - 1.57: 20435 1.57 - 1.70: 0 1.70 - 1.83: 255 Bond restraints: 37054 Sorted by residual: bond pdb=" C ARG D 111 " pdb=" N TYR D 112 " ideal model delta sigma weight residual 1.332 1.475 -0.143 1.40e-02 5.10e+03 1.04e+02 bond pdb=" C PRO A 449 " pdb=" N LEU A 450 " ideal model delta sigma weight residual 1.335 1.441 -0.106 1.34e-02 5.57e+03 6.28e+01 bond pdb=" C PRO B 449 " pdb=" N LEU B 450 " ideal model delta sigma weight residual 1.335 1.441 -0.106 1.34e-02 5.57e+03 6.26e+01 bond pdb=" C PRO C 449 " pdb=" N LEU C 450 " ideal model delta sigma weight residual 1.335 1.441 -0.106 1.34e-02 5.57e+03 6.26e+01 bond pdb=" C VAL C 575 " pdb=" N GLN C 576 " ideal model delta sigma weight residual 1.330 1.428 -0.098 1.32e-02 5.74e+03 5.52e+01 ... (remaining 37049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 48750 3.51 - 7.01: 1534 7.01 - 10.52: 81 10.52 - 14.02: 11 14.02 - 17.53: 2 Bond angle restraints: 50378 Sorted by residual: angle pdb=" N VAL B 714 " pdb=" CA VAL B 714 " pdb=" C VAL B 714 " ideal model delta sigma weight residual 112.12 102.71 9.41 8.40e-01 1.42e+00 1.26e+02 angle pdb=" N ILE A 997 " pdb=" CA ILE A 997 " pdb=" C ILE A 997 " ideal model delta sigma weight residual 113.00 99.89 13.11 1.30e+00 5.92e-01 1.02e+02 angle pdb=" N SER A 695 " pdb=" CA SER A 695 " pdb=" C SER A 695 " ideal model delta sigma weight residual 113.97 102.18 11.79 1.28e+00 6.10e-01 8.49e+01 angle pdb=" N PRO F 165 " pdb=" CA PRO F 165 " pdb=" C PRO F 165 " ideal model delta sigma weight residual 113.53 125.48 -11.95 1.39e+00 5.18e-01 7.39e+01 angle pdb=" N SER B 692 " pdb=" CA SER B 692 " pdb=" C SER B 692 " ideal model delta sigma weight residual 112.93 103.33 9.60 1.12e+00 7.97e-01 7.35e+01 ... (remaining 50373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 19965 18.04 - 36.09: 1539 36.09 - 54.13: 431 54.13 - 72.17: 118 72.17 - 90.22: 18 Dihedral angle restraints: 22071 sinusoidal: 8368 harmonic: 13703 Sorted by residual: dihedral pdb=" CB CYS B1106 " pdb=" SG CYS B1106 " pdb=" SG CYS B1117 " pdb=" CB CYS B1117 " ideal model delta sinusoidal sigma weight residual 93.00 -176.78 -90.22 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS C1106 " pdb=" SG CYS C1106 " pdb=" SG CYS C1117 " pdb=" CB CYS C1117 " ideal model delta sinusoidal sigma weight residual 93.00 170.12 -77.12 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" C TYR C 642 " pdb=" N TYR C 642 " pdb=" CA TYR C 642 " pdb=" CB TYR C 642 " ideal model delta harmonic sigma weight residual -122.60 -143.14 20.54 0 2.50e+00 1.60e-01 6.75e+01 ... (remaining 22068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4929 0.150 - 0.300: 688 0.300 - 0.450: 54 0.450 - 0.600: 1 0.600 - 0.751: 3 Chirality restraints: 5675 Sorted by residual: chirality pdb=" CA TYR C 642 " pdb=" N TYR C 642 " pdb=" C TYR C 642 " pdb=" CB TYR C 642 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CA TYR C 641 " pdb=" N TYR C 641 " pdb=" C TYR C 641 " pdb=" CB TYR C 641 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA THR B1077 " pdb=" N THR B1077 " pdb=" C THR B1077 " pdb=" CB THR B1077 " both_signs ideal model delta sigma weight residual False 2.53 1.87 0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 5672 not shown) Planarity restraints: 6483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASER A 51 " 0.030 2.00e-02 2.50e+03 6.27e-02 3.94e+01 pdb=" C ASER A 51 " -0.108 2.00e-02 2.50e+03 pdb=" O ASER A 51 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS A 52 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BSER A 51 " 0.030 2.00e-02 2.50e+03 6.16e-02 3.79e+01 pdb=" C BSER A 51 " -0.107 2.00e-02 2.50e+03 pdb=" O BSER A 51 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS A 52 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 323 " -0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C PHE C 323 " 0.069 2.00e-02 2.50e+03 pdb=" O PHE C 323 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU C 324 " -0.023 2.00e-02 2.50e+03 ... (remaining 6480 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 549 2.64 - 3.21: 33309 3.21 - 3.77: 56183 3.77 - 4.34: 78345 4.34 - 4.90: 122663 Nonbonded interactions: 291049 Sorted by model distance: nonbonded pdb=" OH TYR A 184 " pdb=" OD2 ASP A 288 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR C 58 " pdb=" O GLY C 331 " model vdw 2.100 3.040 nonbonded pdb=" OH TYR B 58 " pdb=" O GLY B 331 " model vdw 2.110 3.040 nonbonded pdb=" O THR C 212 " pdb=" OG SER C 215 " model vdw 2.113 3.040 nonbonded pdb=" O SER A 88 " pdb=" OG SER A 299 " model vdw 2.167 3.040 ... (remaining 291044 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 18 through 50 or resid 52 through 60 or resid 63 through 4 \ 21 or (resid 422 and (name N or name CA or name C or name O or name CB )) or res \ id 423 through 480 or (resid 481 through 482 and (name N or name CA or name C or \ name O or name CB )) or resid 483 through 641 or (resid 642 and (name N or name \ CA or name C or name O or name CB )) or resid 643 through 676 or resid 678 thro \ ugh 1043 or resid 1045 through 1164 or resid 1171 through 1178 or resid 1182 thr \ ough 1206)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 86 or resid 88 through 4 \ 21 or (resid 422 and (name N or name CA or name C or name O or name CB )) or res \ id 423 through 480 or (resid 481 through 482 and (name N or name CA or name C or \ name O or name CB )) or resid 483 through 586 or resid 596 through 676 or resid \ 678 through 690 or resid 692 through 723 or (resid 724 through 725 and (name N \ or name CA or name C or name O or name CB )) or resid 726 through 743 or resid 7 \ 57 or (resid 758 through 760 and (name N or name CA or name C or name O or name \ CB )) or resid 761 through 1164 or resid 1171 through 1173 or resid 1175 through \ 1178 or resid 1182 through 1206)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 60 or resid 63 through 5 \ 86 or resid 596 through 641 or (resid 642 and (name N or name CA or name C or na \ me O or name CB )) or resid 643 through 690 or resid 692 through 723 or (resid 7 \ 24 through 725 and (name N or name CA or name C or name O or name CB )) or resid \ 726 through 743 or resid 757 or (resid 758 through 760 and (name N or name CA o \ r name C or name O or name CB )) or resid 761 through 1043 or resid 1045 through \ 1206)) } ncs_group { reference = (chain 'D' and (resid 4 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 229)) selection = (chain 'F' and (resid 4 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 229)) selection = chain 'H' } ncs_group { reference = (chain 'E' and resid 4 through 215) selection = (chain 'G' and resid 4 through 215) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 45.230 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 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 : 0.012 0.143 37102 Z= 0.885 Angle : 1.551 17.526 50474 Z= 1.103 Chirality : 0.103 0.751 5675 Planarity : 0.006 0.084 6483 Dihedral : 14.532 89.898 13161 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 1.88 % Allowed : 10.21 % Favored : 87.91 % Rotamer: Outliers : 7.18 % Allowed : 8.34 % Favored : 84.48 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.12), residues: 4641 helix: 0.62 (0.19), residues: 725 sheet: 0.40 (0.16), residues: 1168 loop : -1.94 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1057 TYR 0.046 0.003 TYR C 77 PHE 0.046 0.003 PHE C1136 TRP 0.025 0.002 TRP C 310 HIS 0.010 0.002 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.01246 (37054) covalent geometry : angle 1.54918 (50378) SS BOND : bond 0.01171 ( 48) SS BOND : angle 2.31047 ( 96) hydrogen bonds : bond 0.20299 ( 1200) hydrogen bonds : angle 8.84608 ( 3258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 516 time to evaluate : 1.379 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: A 100 LEU cc_start: 0.6847 (mp) cc_final: 0.6624 (mt) REVERT: A 240 MET cc_start: 0.6732 (pmm) cc_final: 0.6331 (pmm) REVERT: A 484 VAL cc_start: 0.1675 (OUTLIER) cc_final: 0.1327 (p) REVERT: A 629 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6691 (mmt90) REVERT: A 940 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7837 (p0) REVERT: B 101 PHE cc_start: 0.6716 (m-10) cc_final: 0.6511 (m-80) REVERT: B 161 MET cc_start: 0.5920 (mmp) cc_final: 0.5635 (mmt) REVERT: B 218 ASN cc_start: 0.7291 (t0) cc_final: 0.7091 (t0) REVERT: B 240 MET cc_start: 0.7658 (tpp) cc_final: 0.7235 (tpp) REVERT: B 483 THR cc_start: 0.3914 (OUTLIER) cc_final: 0.3690 (p) REVERT: B 1008 MET cc_start: 0.7842 (ttp) cc_final: 0.7377 (ttp) REVERT: B 1056 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6196 (mp10) REVERT: B 1173 ILE cc_start: 0.5430 (tp) cc_final: 0.5130 (pt) REVERT: C 183 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6455 (p90) REVERT: C 208 HIS cc_start: 0.6087 (p90) cc_final: 0.5711 (p-80) REVERT: C 486 HIS cc_start: 0.3960 (OUTLIER) cc_final: 0.2469 (t70) REVERT: C 960 TRP cc_start: 0.6519 (OUTLIER) cc_final: 0.5162 (t60) REVERT: C 1043 THR cc_start: 0.5498 (OUTLIER) cc_final: 0.5106 (p) REVERT: D 48 LEU cc_start: -0.0695 (OUTLIER) cc_final: -0.1053 (tt) REVERT: F 23 VAL cc_start: 0.3733 (OUTLIER) cc_final: 0.3476 (m) REVERT: F 51 MET cc_start: 0.3161 (OUTLIER) cc_final: 0.1409 (ppp) REVERT: F 84 MET cc_start: 0.1668 (tmm) cc_final: 0.1034 (tmm) REVERT: F 103 TYR cc_start: 0.2741 (t80) cc_final: 0.2117 (t80) REVERT: F 112 TYR cc_start: 0.4764 (OUTLIER) cc_final: 0.4157 (t80) REVERT: F 170 VAL cc_start: 0.0451 (OUTLIER) cc_final: 0.0028 (t) REVERT: F 200 VAL cc_start: 0.4761 (m) cc_final: 0.4384 (p) REVERT: G 97 TYR cc_start: 0.1019 (OUTLIER) cc_final: -0.0381 (p90) REVERT: G 150 VAL cc_start: 0.0703 (OUTLIER) cc_final: 0.0133 (m) REVERT: G 153 LYS cc_start: 0.0616 (OUTLIER) cc_final: -0.0374 (mmmt) REVERT: G 213 PHE cc_start: -0.0447 (OUTLIER) cc_final: -0.2038 (m-10) REVERT: H 202 VAL cc_start: 0.1461 (OUTLIER) cc_final: 0.1245 (p) REVERT: I 97 TYR cc_start: 0.1451 (OUTLIER) cc_final: -0.0317 (p90) REVERT: I 153 LYS cc_start: 0.1417 (OUTLIER) cc_final: 0.0711 (mmmt) REVERT: I 213 PHE cc_start: -0.1075 (OUTLIER) cc_final: -0.2053 (t80) outliers start: 291 outliers final: 55 residues processed: 745 average time/residue: 0.2147 time to fit residues: 267.3780 Evaluate side-chains 344 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 267 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1125 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PRO Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 112 TYR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 213 PHE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 LYS Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 599 GLN A 812 ASN A 993 ASN A 999 ASN A1027 ASN A1056 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1169 ASN A1176 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN B 167 HIS B 346 GLN B 408 ASN B1016 ASN B1056 GLN B1072 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN B1163 ASN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN C 421 ASN C 647 ASN C 719 ASN C 812 ASN C 842 GLN ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 GLN C1146 HIS D 6 GLN D 108 ASN D 114 GLN D 189 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 93 GLN E 96 ASN E 128 GLN E 142 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 HIS G 96 ASN G 128 GLN G 142 ASN G 164 GLN H 210 GLN I 93 GLN I 96 ASN I 142 ASN I 164 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.150068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.119995 restraints weight = 231600.249| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 7.69 r_work: 0.3544 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 37102 Z= 0.188 Angle : 0.803 12.060 50474 Z= 0.426 Chirality : 0.049 0.294 5675 Planarity : 0.005 0.060 6483 Dihedral : 7.692 58.247 5205 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.81 % Favored : 90.65 % Rotamer: Outliers : 3.48 % Allowed : 12.69 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.25 (0.12), residues: 4641 helix: 0.72 (0.19), residues: 769 sheet: 0.37 (0.16), residues: 1184 loop : -1.98 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 694 TYR 0.031 0.002 TYR B 641 PHE 0.025 0.002 PHE A 101 TRP 0.025 0.002 TRP I 35 HIS 0.008 0.002 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00414 (37054) covalent geometry : angle 0.80168 (50378) SS BOND : bond 0.00636 ( 48) SS BOND : angle 1.29580 ( 96) hydrogen bonds : bond 0.05755 ( 1200) hydrogen bonds : angle 6.61855 ( 3258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 303 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 HIS cc_start: 0.4515 (OUTLIER) cc_final: 0.4218 (p-80) REVERT: A 563 MET cc_start: 0.1387 (mtm) cc_final: 0.0933 (ttp) REVERT: A 899 THR cc_start: 0.8175 (p) cc_final: 0.7961 (t) REVERT: A 940 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8206 (p0) REVERT: A 960 TRP cc_start: 0.5912 (t-100) cc_final: 0.1922 (t-100) REVERT: B 101 PHE cc_start: 0.7315 (m-10) cc_final: 0.6607 (m-80) REVERT: B 161 MET cc_start: 0.5807 (mmp) cc_final: 0.5553 (mmt) REVERT: B 375 VAL cc_start: 0.8347 (t) cc_final: 0.8029 (p) REVERT: B 563 MET cc_start: 0.2261 (OUTLIER) cc_final: 0.1031 (ttp) REVERT: B 688 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7451 (mp-120) REVERT: B 723 PHE cc_start: 0.6581 (t80) cc_final: 0.6296 (t80) REVERT: B 842 GLN cc_start: 0.8379 (tp40) cc_final: 0.8125 (tp40) REVERT: B 987 GLN cc_start: 0.7254 (tt0) cc_final: 0.5753 (tt0) REVERT: B 1173 ILE cc_start: 0.6061 (tp) cc_final: 0.5481 (pt) REVERT: B 1180 ILE cc_start: 0.5979 (tp) cc_final: 0.5777 (tp) REVERT: B 1192 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.4040 (m-80) REVERT: C 183 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7154 (p90) REVERT: C 563 MET cc_start: 0.2859 (mtp) cc_final: 0.0627 (ptp) REVERT: C 865 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: C 960 TRP cc_start: 0.7130 (OUTLIER) cc_final: 0.5656 (t60) REVERT: C 1008 MET cc_start: 0.8298 (ttm) cc_final: 0.7514 (tpp) REVERT: C 1043 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6462 (p) REVERT: C 1201 ASN cc_start: 0.7297 (t0) cc_final: 0.6930 (t0) REVERT: D 32 PHE cc_start: 0.5941 (m-80) cc_final: 0.5685 (m-80) REVERT: E 92 GLN cc_start: 0.1323 (OUTLIER) cc_final: 0.0999 (tp40) REVERT: E 139 LEU cc_start: 0.2133 (OUTLIER) cc_final: 0.1822 (mp) REVERT: F 51 MET cc_start: 0.1860 (OUTLIER) cc_final: 0.1324 (ppp) REVERT: F 103 TYR cc_start: 0.5766 (t80) cc_final: 0.5565 (t80) REVERT: F 187 VAL cc_start: -0.1028 (OUTLIER) cc_final: -0.1256 (t) REVERT: F 200 VAL cc_start: 0.4927 (m) cc_final: 0.4560 (p) REVERT: G 27 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7424 (mmt-90) REVERT: G 97 TYR cc_start: 0.1820 (OUTLIER) cc_final: 0.0150 (p90) REVERT: G 110 ILE cc_start: 0.0929 (OUTLIER) cc_final: 0.0616 (pt) REVERT: G 153 LYS cc_start: 0.1799 (OUTLIER) cc_final: 0.0814 (mmmm) REVERT: G 203 GLN cc_start: 0.1288 (mp10) cc_final: 0.0905 (tt0) REVERT: G 213 PHE cc_start: -0.1183 (OUTLIER) cc_final: -0.2181 (m-10) REVERT: I 94 TYR cc_start: 0.0669 (p90) cc_final: -0.0059 (p90) REVERT: I 97 TYR cc_start: 0.1284 (OUTLIER) cc_final: -0.0157 (p90) REVERT: I 187 LYS cc_start: 0.2521 (mmtm) cc_final: 0.2122 (tptp) REVERT: I 213 PHE cc_start: -0.1008 (OUTLIER) cc_final: -0.1849 (t80) outliers start: 141 outliers final: 64 residues processed: 423 average time/residue: 0.2166 time to fit residues: 155.1750 Evaluate side-chains 325 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 242 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1179 ARG Chi-restraints excluded: chain B residue 1192 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 213 PHE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 341 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 269 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 375 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 79 optimal weight: 0.0370 chunk 18 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 681 HIS A 987 GLN A1020 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 ASN C1023 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1160 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN I 159 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.147223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111258 restraints weight = 200659.734| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 6.30 r_work: 0.3499 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 37102 Z= 0.193 Angle : 0.769 11.582 50474 Z= 0.407 Chirality : 0.049 0.261 5675 Planarity : 0.005 0.050 6483 Dihedral : 6.928 59.212 5137 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.21 % Favored : 89.31 % Rotamer: Outliers : 3.38 % Allowed : 13.60 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.31 (0.12), residues: 4641 helix: 0.80 (0.19), residues: 752 sheet: 0.19 (0.15), residues: 1207 loop : -1.98 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 235 TYR 0.038 0.002 TYR B 641 PHE 0.032 0.002 PHE A 778 TRP 0.029 0.002 TRP I 35 HIS 0.007 0.001 HIS B1138 Details of bonding type rmsd covalent geometry : bond 0.00434 (37054) covalent geometry : angle 0.76721 (50378) SS BOND : bond 0.00471 ( 48) SS BOND : angle 1.37449 ( 96) hydrogen bonds : bond 0.05324 ( 1200) hydrogen bonds : angle 6.14301 ( 3258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 271 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 455 ASP cc_start: 0.2329 (t0) cc_final: 0.2113 (m-30) REVERT: A 960 TRP cc_start: 0.5884 (t-100) cc_final: 0.2086 (t-100) REVERT: A 990 LEU cc_start: 0.8669 (mt) cc_final: 0.8364 (tt) REVERT: B 161 MET cc_start: 0.5898 (mmp) cc_final: 0.5624 (mmt) REVERT: B 367 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7908 (pp20) REVERT: B 375 VAL cc_start: 0.8395 (t) cc_final: 0.8137 (p) REVERT: B 596 ILE cc_start: 0.8773 (mm) cc_final: 0.8509 (mt) REVERT: B 688 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7507 (mp-120) REVERT: B 1173 ILE cc_start: 0.5987 (tp) cc_final: 0.5339 (pt) REVERT: B 1180 ILE cc_start: 0.5703 (OUTLIER) cc_final: 0.5121 (tp) REVERT: C 164 PHE cc_start: 0.3468 (m-80) cc_final: 0.3205 (m-80) REVERT: C 183 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6971 (p90) REVERT: C 298 HIS cc_start: 0.5814 (OUTLIER) cc_final: 0.5496 (p90) REVERT: C 563 MET cc_start: 0.2877 (mtp) cc_final: 0.2062 (mtt) REVERT: C 865 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: C 960 TRP cc_start: 0.7177 (OUTLIER) cc_final: 0.5510 (t60) REVERT: C 1043 THR cc_start: 0.7261 (OUTLIER) cc_final: 0.6882 (p) REVERT: D 32 PHE cc_start: 0.5806 (m-80) cc_final: 0.5466 (m-80) REVERT: D 60 THR cc_start: 0.2675 (OUTLIER) cc_final: 0.2089 (t) REVERT: F 51 MET cc_start: 0.1229 (OUTLIER) cc_final: 0.0764 (ppp) REVERT: G 97 TYR cc_start: 0.0987 (OUTLIER) cc_final: -0.0104 (p90) REVERT: G 110 ILE cc_start: 0.0529 (OUTLIER) cc_final: 0.0214 (pt) REVERT: G 153 LYS cc_start: 0.1926 (OUTLIER) cc_final: 0.0985 (mmmm) REVERT: G 203 GLN cc_start: 0.1178 (mp10) cc_final: 0.0891 (tt0) REVERT: H 68 GLN cc_start: 0.3220 (mt0) cc_final: 0.2995 (mm-40) REVERT: I 35 TRP cc_start: 0.2829 (m-90) cc_final: 0.2465 (m-10) REVERT: I 97 TYR cc_start: 0.1227 (OUTLIER) cc_final: -0.0158 (p90) REVERT: I 187 LYS cc_start: 0.2763 (mmtm) cc_final: 0.2551 (tptp) outliers start: 137 outliers final: 81 residues processed: 382 average time/residue: 0.2074 time to fit residues: 136.4188 Evaluate side-chains 325 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 230 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1179 ARG Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 298 HIS Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 57 PHE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 411 optimal weight: 30.0000 chunk 297 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 681 HIS ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN B 839 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 ASN C1163 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 193 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.144171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.106919 restraints weight = 193694.960| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 6.00 r_work: 0.3439 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 37102 Z= 0.254 Angle : 0.833 15.781 50474 Z= 0.440 Chirality : 0.052 0.455 5675 Planarity : 0.005 0.059 6483 Dihedral : 7.139 58.437 5123 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.86 % Favored : 88.69 % Rotamer: Outliers : 3.63 % Allowed : 14.61 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.62 (0.12), residues: 4641 helix: 0.43 (0.19), residues: 767 sheet: -0.08 (0.15), residues: 1175 loop : -2.10 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 111 TYR 0.047 0.003 TYR B 641 PHE 0.038 0.003 PHE A 778 TRP 0.016 0.002 TRP B1184 HIS 0.040 0.002 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00578 (37054) covalent geometry : angle 0.83075 (50378) SS BOND : bond 0.01047 ( 48) SS BOND : angle 1.54064 ( 96) hydrogen bonds : bond 0.05566 ( 1200) hydrogen bonds : angle 6.18518 ( 3258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 254 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 ASP cc_start: 0.1896 (t0) cc_final: 0.0704 (m-30) REVERT: A 649 TYR cc_start: 0.8033 (m-10) cc_final: 0.7766 (m-10) REVERT: A 1116 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7555 (p90) REVERT: A 1182 ASP cc_start: 0.7306 (m-30) cc_final: 0.6755 (m-30) REVERT: B 161 MET cc_start: 0.5904 (mmp) cc_final: 0.5583 (mmt) REVERT: B 256 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8989 (mt) REVERT: B 367 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7901 (pp20) REVERT: B 423 PHE cc_start: 0.5459 (t80) cc_final: 0.5137 (t80) REVERT: B 1173 ILE cc_start: 0.5858 (tp) cc_final: 0.5257 (pt) REVERT: C 183 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.6880 (p90) REVERT: C 865 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: C 960 TRP cc_start: 0.7312 (OUTLIER) cc_final: 0.5510 (t60) REVERT: C 1012 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7766 (t80) REVERT: D 9 GLN cc_start: 0.3597 (OUTLIER) cc_final: 0.3356 (mt0) REVERT: D 120 TRP cc_start: 0.2106 (m100) cc_final: 0.1887 (m100) REVERT: E 213 PHE cc_start: -0.0912 (OUTLIER) cc_final: -0.2343 (m-80) REVERT: F 51 MET cc_start: 0.0175 (OUTLIER) cc_final: -0.0058 (ppp) REVERT: G 97 TYR cc_start: 0.1191 (OUTLIER) cc_final: 0.0365 (p90) REVERT: G 110 ILE cc_start: 0.0236 (OUTLIER) cc_final: -0.0008 (pt) REVERT: G 153 LYS cc_start: 0.1970 (OUTLIER) cc_final: 0.1156 (mmmm) REVERT: I 35 TRP cc_start: 0.2513 (m-90) cc_final: 0.1983 (m-90) REVERT: I 78 ILE cc_start: -0.0267 (OUTLIER) cc_final: -0.0643 (pt) REVERT: I 97 TYR cc_start: 0.1402 (OUTLIER) cc_final: -0.0044 (p90) REVERT: I 187 LYS cc_start: 0.2465 (mmtm) cc_final: 0.2256 (tptp) outliers start: 147 outliers final: 93 residues processed: 372 average time/residue: 0.1988 time to fit residues: 127.5411 Evaluate side-chains 341 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 233 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1179 ARG Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 344 optimal weight: 0.9990 chunk 381 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 452 optimal weight: 10.0000 chunk 314 optimal weight: 2.9990 chunk 317 optimal weight: 0.9980 chunk 311 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN B 107 GLN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN B 987 GLN ** B1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** 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 = 0.4497 r_free = 0.4497 target = 0.145091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.111829 restraints weight = 253632.036| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 7.44 r_work: 0.3428 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 37102 Z= 0.175 Angle : 0.737 16.950 50474 Z= 0.387 Chirality : 0.048 0.431 5675 Planarity : 0.005 0.066 6483 Dihedral : 6.618 58.176 5117 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.43 % Favored : 89.18 % Rotamer: Outliers : 3.31 % Allowed : 15.23 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.48 (0.12), residues: 4641 helix: 0.74 (0.19), residues: 744 sheet: -0.04 (0.15), residues: 1221 loop : -2.05 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1113 TYR 0.037 0.002 TYR B 641 PHE 0.040 0.002 PHE A 778 TRP 0.015 0.001 TRP B1184 HIS 0.005 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00397 (37054) covalent geometry : angle 0.73471 (50378) SS BOND : bond 0.00433 ( 48) SS BOND : angle 1.50484 ( 96) hydrogen bonds : bond 0.04973 ( 1200) hydrogen bonds : angle 5.87764 ( 3258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 240 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.3453 (ppp) cc_final: 0.3027 (ppp) REVERT: A 455 ASP cc_start: 0.1586 (t0) cc_final: 0.0952 (m-30) REVERT: A 486 HIS cc_start: 0.4978 (OUTLIER) cc_final: 0.4370 (p-80) REVERT: A 649 TYR cc_start: 0.7955 (m-10) cc_final: 0.7737 (m-80) REVERT: A 728 LYS cc_start: 0.7787 (tptt) cc_final: 0.7581 (tptt) REVERT: A 765 ASN cc_start: 0.5385 (p0) cc_final: 0.4653 (t0) REVERT: A 960 TRP cc_start: 0.6230 (t-100) cc_final: 0.2477 (t-100) REVERT: A 990 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 1182 ASP cc_start: 0.7460 (m-30) cc_final: 0.6836 (m-30) REVERT: B 161 MET cc_start: 0.5990 (mmp) cc_final: 0.5528 (mmt) REVERT: B 240 MET cc_start: 0.7227 (tpp) cc_final: 0.7019 (tpp) REVERT: B 367 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7919 (pp20) REVERT: B 1180 ILE cc_start: 0.6053 (OUTLIER) cc_final: 0.5418 (tp) REVERT: B 1204 TYR cc_start: 0.6702 (m-80) cc_final: 0.6391 (m-80) REVERT: C 183 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6760 (p90) REVERT: C 241 TYR cc_start: 0.7083 (m-80) cc_final: 0.6618 (m-80) REVERT: C 865 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: C 960 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.5718 (t60) REVERT: C 1012 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7759 (t80) REVERT: C 1195 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: D 9 GLN cc_start: 0.1998 (OUTLIER) cc_final: 0.1645 (mt0) REVERT: D 60 THR cc_start: 0.2309 (OUTLIER) cc_final: 0.1797 (t) REVERT: D 120 TRP cc_start: 0.2367 (m100) cc_final: 0.2048 (m100) REVERT: E 213 PHE cc_start: -0.0862 (OUTLIER) cc_final: -0.2313 (m-80) REVERT: F 51 MET cc_start: 0.0752 (OUTLIER) cc_final: 0.0265 (ppp) REVERT: G 97 TYR cc_start: 0.1186 (OUTLIER) cc_final: 0.0288 (p90) REVERT: G 110 ILE cc_start: 0.0872 (OUTLIER) cc_final: 0.0500 (pt) REVERT: G 147 GLU cc_start: 0.3198 (OUTLIER) cc_final: 0.2992 (mp0) REVERT: G 153 LYS cc_start: 0.1845 (OUTLIER) cc_final: 0.1562 (mppt) REVERT: I 35 TRP cc_start: 0.2364 (m-90) cc_final: 0.1954 (m-90) REVERT: I 78 ILE cc_start: 0.0063 (OUTLIER) cc_final: -0.0289 (pt) REVERT: I 97 TYR cc_start: 0.1222 (OUTLIER) cc_final: -0.0421 (p90) REVERT: I 187 LYS cc_start: 0.2203 (mmtm) cc_final: 0.1946 (tptp) outliers start: 134 outliers final: 87 residues processed: 357 average time/residue: 0.1964 time to fit residues: 121.7855 Evaluate side-chains 326 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 220 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1179 ARG Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 87 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 402 optimal weight: 8.9990 chunk 233 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 340 optimal weight: 20.0000 chunk 355 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 117 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN A 857 GLN B 842 GLN ** B1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 128 GLN E 170 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.144540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.104250 restraints weight = 161667.664| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 5.42 r_work: 0.3391 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 37102 Z= 0.243 Angle : 0.815 16.174 50474 Z= 0.431 Chirality : 0.051 0.495 5675 Planarity : 0.005 0.065 6483 Dihedral : 6.968 58.747 5112 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.87 % Favored : 87.78 % Rotamer: Outliers : 3.75 % Allowed : 15.75 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.65 (0.12), residues: 4641 helix: 0.57 (0.19), residues: 740 sheet: -0.18 (0.15), residues: 1192 loop : -2.12 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1113 TYR 0.044 0.002 TYR B 641 PHE 0.041 0.002 PHE B 232 TRP 0.014 0.002 TRP B 310 HIS 0.008 0.002 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00557 (37054) covalent geometry : angle 0.81283 (50378) SS BOND : bond 0.00606 ( 48) SS BOND : angle 1.48795 ( 96) hydrogen bonds : bond 0.05435 ( 1200) hydrogen bonds : angle 6.02229 ( 3258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 238 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.3696 (ppp) cc_final: 0.3217 (ppp) REVERT: A 455 ASP cc_start: 0.1131 (t0) cc_final: 0.0318 (m-30) REVERT: A 486 HIS cc_start: 0.5046 (OUTLIER) cc_final: 0.4295 (p-80) REVERT: A 728 LYS cc_start: 0.7802 (tptt) cc_final: 0.7542 (tptt) REVERT: A 765 ASN cc_start: 0.5227 (p0) cc_final: 0.4386 (t0) REVERT: A 796 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.6797 (tp40) REVERT: B 161 MET cc_start: 0.6113 (mmp) cc_final: 0.5695 (mmt) REVERT: B 239 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: B 367 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7850 (pp20) REVERT: B 1204 TYR cc_start: 0.6901 (m-80) cc_final: 0.6407 (m-80) REVERT: C 183 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.6947 (p90) REVERT: C 569 MET cc_start: 0.0945 (mtm) cc_final: -0.0033 (mmp) REVERT: C 582 ASN cc_start: 0.4166 (t0) cc_final: 0.3695 (t0) REVERT: C 865 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: C 960 TRP cc_start: 0.7328 (OUTLIER) cc_final: 0.5801 (t60) REVERT: C 1012 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7788 (t80) REVERT: C 1195 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: D 9 GLN cc_start: 0.3295 (OUTLIER) cc_final: 0.2932 (mt0) REVERT: D 60 THR cc_start: 0.2474 (OUTLIER) cc_final: 0.2067 (t) REVERT: D 120 TRP cc_start: 0.2256 (m100) cc_final: 0.1996 (m100) REVERT: E 213 PHE cc_start: -0.1101 (OUTLIER) cc_final: -0.2468 (m-80) REVERT: F 76 ASP cc_start: 0.6251 (t70) cc_final: 0.5597 (m-30) REVERT: G 97 TYR cc_start: 0.1414 (OUTLIER) cc_final: 0.0971 (p90) REVERT: G 147 GLU cc_start: 0.3279 (OUTLIER) cc_final: 0.3042 (mp0) REVERT: G 205 LEU cc_start: 0.1095 (mt) cc_final: 0.0429 (pp) REVERT: I 35 TRP cc_start: 0.2340 (m-90) cc_final: 0.1742 (m-90) REVERT: I 72 THR cc_start: 0.3906 (OUTLIER) cc_final: 0.3684 (m) REVERT: I 97 TYR cc_start: 0.1297 (OUTLIER) cc_final: -0.0375 (p90) outliers start: 152 outliers final: 99 residues processed: 367 average time/residue: 0.1942 time to fit residues: 125.2654 Evaluate side-chains 342 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 227 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 277 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 341 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 438 optimal weight: 0.0050 chunk 447 optimal weight: 0.9980 chunk 310 optimal weight: 3.9990 chunk 297 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN B1027 ASN C 772 GLN ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN D 189 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.145994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.119117 restraints weight = 226002.290| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 4.74 r_work: 0.3523 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 37102 Z= 0.134 Angle : 0.701 15.688 50474 Z= 0.364 Chirality : 0.046 0.351 5675 Planarity : 0.005 0.120 6483 Dihedral : 6.224 57.315 5104 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.48 % Favored : 90.18 % Rotamer: Outliers : 2.86 % Allowed : 16.56 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.40 (0.12), residues: 4641 helix: 1.06 (0.20), residues: 728 sheet: -0.11 (0.15), residues: 1237 loop : -2.01 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B1179 TYR 0.036 0.002 TYR B 641 PHE 0.035 0.002 PHE A 778 TRP 0.022 0.001 TRP E 35 HIS 0.005 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00289 (37054) covalent geometry : angle 0.69916 (50378) SS BOND : bond 0.00380 ( 48) SS BOND : angle 1.28605 ( 96) hydrogen bonds : bond 0.04521 ( 1200) hydrogen bonds : angle 5.63755 ( 3258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 246 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.3527 (ppp) cc_final: 0.2957 (ppp) REVERT: A 455 ASP cc_start: 0.1441 (t0) cc_final: 0.0436 (m-30) REVERT: A 486 HIS cc_start: 0.5264 (OUTLIER) cc_final: 0.4396 (p-80) REVERT: A 765 ASN cc_start: 0.5153 (p0) cc_final: 0.4435 (t0) REVERT: A 796 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: A 960 TRP cc_start: 0.6103 (t-100) cc_final: 0.1444 (t-100) REVERT: A 1182 ASP cc_start: 0.7607 (m-30) cc_final: 0.7148 (m-30) REVERT: B 161 MET cc_start: 0.5767 (mmp) cc_final: 0.5313 (mmt) REVERT: B 232 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6626 (t80) REVERT: B 1180 ILE cc_start: 0.5256 (OUTLIER) cc_final: 0.3626 (tp) REVERT: B 1195 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: C 183 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7286 (p90) REVERT: C 563 MET cc_start: 0.2696 (mtp) cc_final: 0.0356 (ptp) REVERT: C 569 MET cc_start: 0.0979 (mtm) cc_final: 0.0116 (mmp) REVERT: C 582 ASN cc_start: 0.4580 (t0) cc_final: 0.3436 (t0) REVERT: C 696 MET cc_start: 0.6834 (tpt) cc_final: 0.6552 (tpt) REVERT: C 865 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: C 960 TRP cc_start: 0.7203 (OUTLIER) cc_final: 0.5359 (t60) REVERT: C 1012 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7723 (t80) REVERT: D 60 THR cc_start: 0.2112 (OUTLIER) cc_final: 0.1700 (t) REVERT: D 120 TRP cc_start: 0.2494 (m100) cc_final: 0.2099 (m100) REVERT: F 49 GLU cc_start: 0.3456 (tp30) cc_final: 0.2248 (tt0) REVERT: F 76 ASP cc_start: 0.6266 (t70) cc_final: 0.5482 (m-30) REVERT: F 84 MET cc_start: 0.2566 (ttp) cc_final: 0.1471 (tmm) REVERT: G 97 TYR cc_start: 0.1144 (OUTLIER) cc_final: 0.0642 (p90) REVERT: G 170 GLN cc_start: 0.1509 (OUTLIER) cc_final: 0.1161 (tm-30) REVERT: G 205 LEU cc_start: 0.0457 (mt) cc_final: 0.0081 (pp) REVERT: G 213 PHE cc_start: -0.0835 (OUTLIER) cc_final: -0.2414 (m-10) REVERT: I 35 TRP cc_start: 0.2212 (m-90) cc_final: 0.1591 (m-90) REVERT: I 97 TYR cc_start: 0.1047 (OUTLIER) cc_final: -0.0496 (p90) outliers start: 116 outliers final: 80 residues processed: 347 average time/residue: 0.1916 time to fit residues: 116.4395 Evaluate side-chains 319 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 225 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 170 GLN Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 213 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 290 optimal weight: 0.5980 chunk 411 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 226 optimal weight: 20.0000 chunk 218 optimal weight: 0.8980 chunk 282 optimal weight: 7.9990 chunk 86 optimal weight: 0.0670 chunk 75 optimal weight: 0.0980 chunk 2 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN B 987 GLN ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1042 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN H 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.147041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.117764 restraints weight = 244766.208| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 7.23 r_work: 0.3480 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 37102 Z= 0.124 Angle : 0.684 16.438 50474 Z= 0.353 Chirality : 0.045 0.344 5675 Planarity : 0.004 0.063 6483 Dihedral : 5.902 56.303 5103 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.72 % Favored : 89.94 % Rotamer: Outliers : 2.47 % Allowed : 17.23 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.24 (0.12), residues: 4641 helix: 1.21 (0.20), residues: 726 sheet: 0.01 (0.15), residues: 1233 loop : -1.92 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1179 TYR 0.049 0.001 TYR B 641 PHE 0.032 0.001 PHE B 232 TRP 0.020 0.001 TRP E 35 HIS 0.004 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00262 (37054) covalent geometry : angle 0.68178 (50378) SS BOND : bond 0.00415 ( 48) SS BOND : angle 1.32347 ( 96) hydrogen bonds : bond 0.04244 ( 1200) hydrogen bonds : angle 5.48618 ( 3258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 233 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.3588 (ppp) cc_final: 0.3046 (ppp) REVERT: A 455 ASP cc_start: 0.1415 (t0) cc_final: 0.0449 (m-30) REVERT: A 729 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.5179 (mt) REVERT: A 765 ASN cc_start: 0.5334 (p0) cc_final: 0.4542 (t0) REVERT: A 960 TRP cc_start: 0.6363 (t-100) cc_final: 0.1675 (t-100) REVERT: B 161 MET cc_start: 0.5748 (mmp) cc_final: 0.5185 (mmt) REVERT: B 232 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6189 (t80) REVERT: B 1180 ILE cc_start: 0.5712 (OUTLIER) cc_final: 0.5062 (tp) REVERT: C 183 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7267 (p90) REVERT: C 224 SER cc_start: 0.7244 (m) cc_final: 0.6794 (t) REVERT: C 563 MET cc_start: 0.2923 (mtp) cc_final: 0.0590 (ptt) REVERT: C 569 MET cc_start: 0.1034 (mtm) cc_final: 0.0199 (mmp) REVERT: C 696 MET cc_start: 0.6724 (tpt) cc_final: 0.6510 (tpt) REVERT: C 865 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: C 960 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.5457 (t60) REVERT: C 1012 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7809 (t80) REVERT: C 1044 PHE cc_start: 0.6707 (t80) cc_final: 0.6442 (t80) REVERT: C 1113 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7859 (ttt180) REVERT: D 60 THR cc_start: 0.2279 (OUTLIER) cc_final: 0.1873 (t) REVERT: D 120 TRP cc_start: 0.2258 (m100) cc_final: 0.1942 (m100) REVERT: E 102 PHE cc_start: 0.3654 (OUTLIER) cc_final: 0.2850 (m-80) REVERT: E 213 PHE cc_start: -0.1194 (OUTLIER) cc_final: -0.2471 (m-80) REVERT: F 49 GLU cc_start: 0.3540 (tp30) cc_final: 0.2407 (tt0) REVERT: F 76 ASP cc_start: 0.6266 (t70) cc_final: 0.5592 (m-30) REVERT: F 112 TYR cc_start: 0.4832 (OUTLIER) cc_final: 0.4167 (t80) REVERT: G 97 TYR cc_start: 0.1457 (OUTLIER) cc_final: 0.1125 (p90) REVERT: G 147 GLU cc_start: 0.3312 (OUTLIER) cc_final: 0.3052 (mp0) REVERT: G 205 LEU cc_start: 0.0886 (mt) cc_final: 0.0337 (pp) REVERT: G 213 PHE cc_start: -0.0894 (OUTLIER) cc_final: -0.2393 (m-10) REVERT: I 35 TRP cc_start: 0.2254 (m-90) cc_final: 0.1914 (m-90) REVERT: I 94 TYR cc_start: 0.1189 (p90) cc_final: 0.0291 (p90) REVERT: I 97 TYR cc_start: 0.1037 (OUTLIER) cc_final: -0.0496 (p90) outliers start: 100 outliers final: 73 residues processed: 319 average time/residue: 0.1960 time to fit residues: 109.2719 Evaluate side-chains 311 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 223 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 112 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 213 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 95 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 323 optimal weight: 0.0040 chunk 239 optimal weight: 20.0000 chunk 327 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 268 optimal weight: 20.0000 chunk 385 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 GLN ** 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 = 0.4522 r_free = 0.4522 target = 0.148568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.116581 restraints weight = 209664.190| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 5.74 r_work: 0.3532 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 37102 Z= 0.160 Angle : 0.775 59.199 50474 Z= 0.421 Chirality : 0.046 0.333 5675 Planarity : 0.005 0.123 6483 Dihedral : 5.827 56.230 5099 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.61 % Favored : 90.05 % Rotamer: Outliers : 2.32 % Allowed : 17.28 % Favored : 80.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.23 (0.12), residues: 4641 helix: 1.21 (0.20), residues: 726 sheet: 0.02 (0.15), residues: 1233 loop : -1.91 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1074 TYR 0.053 0.002 TYR B 87 PHE 0.031 0.001 PHE B 232 TRP 0.016 0.001 TRP E 35 HIS 0.011 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00335 (37054) covalent geometry : angle 0.77307 (50378) SS BOND : bond 0.00392 ( 48) SS BOND : angle 1.42630 ( 96) hydrogen bonds : bond 0.04263 ( 1200) hydrogen bonds : angle 5.48533 ( 3258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 224 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.3516 (ppp) cc_final: 0.2966 (ppp) REVERT: A 455 ASP cc_start: 0.1442 (t0) cc_final: 0.0476 (m-30) REVERT: A 765 ASN cc_start: 0.5228 (p0) cc_final: 0.4384 (t0) REVERT: A 960 TRP cc_start: 0.6123 (t-100) cc_final: 0.1694 (t-100) REVERT: B 161 MET cc_start: 0.5799 (mmp) cc_final: 0.5247 (mmt) REVERT: B 232 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 1180 ILE cc_start: 0.5681 (OUTLIER) cc_final: 0.5093 (tp) REVERT: C 183 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7304 (p90) REVERT: C 224 SER cc_start: 0.7240 (m) cc_final: 0.6769 (t) REVERT: C 563 MET cc_start: 0.2909 (mtp) cc_final: 0.0562 (ptt) REVERT: C 569 MET cc_start: 0.1023 (mtm) cc_final: 0.0187 (mmp) REVERT: C 865 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: C 960 TRP cc_start: 0.7197 (OUTLIER) cc_final: 0.5423 (t60) REVERT: C 1012 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7739 (t80) REVERT: C 1044 PHE cc_start: 0.6547 (t80) cc_final: 0.6346 (t80) REVERT: C 1195 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: D 60 THR cc_start: 0.2243 (OUTLIER) cc_final: 0.1831 (t) REVERT: E 102 PHE cc_start: 0.3729 (OUTLIER) cc_final: 0.2877 (m-80) REVERT: E 213 PHE cc_start: -0.1213 (OUTLIER) cc_final: -0.2460 (m-80) REVERT: F 49 GLU cc_start: 0.3516 (tp30) cc_final: 0.2319 (tt0) REVERT: F 76 ASP cc_start: 0.6323 (t70) cc_final: 0.5589 (m-30) REVERT: F 112 TYR cc_start: 0.4783 (OUTLIER) cc_final: 0.4098 (t80) REVERT: G 97 TYR cc_start: 0.1301 (OUTLIER) cc_final: 0.0961 (p90) REVERT: G 205 LEU cc_start: 0.0644 (mt) cc_final: 0.0190 (pp) REVERT: G 213 PHE cc_start: -0.0854 (OUTLIER) cc_final: -0.2364 (m-10) REVERT: I 35 TRP cc_start: 0.2305 (m-90) cc_final: 0.1936 (m-90) REVERT: I 94 TYR cc_start: 0.1203 (p90) cc_final: 0.0313 (p90) REVERT: I 97 TYR cc_start: 0.1012 (OUTLIER) cc_final: -0.0500 (p90) outliers start: 94 outliers final: 75 residues processed: 303 average time/residue: 0.1993 time to fit residues: 105.7510 Evaluate side-chains 309 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 220 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 987 GLN Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 112 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 213 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 23 optimal weight: 6.9990 chunk 390 optimal weight: 20.0000 chunk 382 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 360 optimal weight: 20.0000 chunk 205 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 391 optimal weight: 0.0370 chunk 341 optimal weight: 5.9990 chunk 346 optimal weight: 20.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 GLN ** 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 = 0.4522 r_free = 0.4522 target = 0.146800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.115018 restraints weight = 216591.965| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 6.79 r_work: 0.3486 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 37102 Z= 0.160 Angle : 0.775 59.199 50474 Z= 0.421 Chirality : 0.046 0.333 5675 Planarity : 0.005 0.123 6483 Dihedral : 5.827 56.230 5099 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.61 % Favored : 90.05 % Rotamer: Outliers : 2.22 % Allowed : 17.37 % Favored : 80.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.23 (0.12), residues: 4641 helix: 1.21 (0.20), residues: 726 sheet: 0.02 (0.15), residues: 1233 loop : -1.91 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1074 TYR 0.053 0.002 TYR B 87 PHE 0.031 0.001 PHE B 232 TRP 0.016 0.001 TRP E 35 HIS 0.011 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00335 (37054) covalent geometry : angle 0.77307 (50378) SS BOND : bond 0.00392 ( 48) SS BOND : angle 1.42630 ( 96) hydrogen bonds : bond 0.04263 ( 1200) hydrogen bonds : angle 5.48533 ( 3258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 220 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.3659 (ppp) cc_final: 0.3083 (ppp) REVERT: A 455 ASP cc_start: 0.1499 (t0) cc_final: 0.0535 (m-30) REVERT: A 765 ASN cc_start: 0.5242 (p0) cc_final: 0.4485 (t0) REVERT: A 960 TRP cc_start: 0.6092 (t-100) cc_final: 0.1689 (t-100) REVERT: B 161 MET cc_start: 0.5977 (mmp) cc_final: 0.5429 (mmt) REVERT: B 232 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6656 (t80) REVERT: B 1180 ILE cc_start: 0.5684 (OUTLIER) cc_final: 0.5201 (tp) REVERT: C 183 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7252 (p90) REVERT: C 224 SER cc_start: 0.7324 (m) cc_final: 0.6892 (t) REVERT: C 563 MET cc_start: 0.3210 (mtp) cc_final: 0.0987 (ptt) REVERT: C 569 MET cc_start: 0.0979 (mtm) cc_final: 0.0144 (mmp) REVERT: C 865 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: C 960 TRP cc_start: 0.7238 (OUTLIER) cc_final: 0.5366 (t60) REVERT: C 1012 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7717 (t80) REVERT: C 1044 PHE cc_start: 0.6794 (t80) cc_final: 0.6496 (t80) REVERT: C 1195 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: D 60 THR cc_start: 0.2286 (OUTLIER) cc_final: 0.1883 (t) REVERT: E 102 PHE cc_start: 0.3733 (OUTLIER) cc_final: 0.2900 (m-80) REVERT: E 213 PHE cc_start: -0.1128 (OUTLIER) cc_final: -0.2415 (m-80) REVERT: F 49 GLU cc_start: 0.3548 (tp30) cc_final: 0.2443 (tt0) REVERT: F 76 ASP cc_start: 0.6321 (t70) cc_final: 0.5569 (m-30) REVERT: F 112 TYR cc_start: 0.4742 (OUTLIER) cc_final: 0.4020 (t80) REVERT: G 97 TYR cc_start: 0.1291 (OUTLIER) cc_final: 0.0966 (p90) REVERT: G 205 LEU cc_start: 0.0588 (mt) cc_final: 0.0161 (pp) REVERT: G 213 PHE cc_start: -0.0829 (OUTLIER) cc_final: -0.2315 (m-10) REVERT: I 35 TRP cc_start: 0.2396 (m-90) cc_final: 0.2029 (m-90) REVERT: I 94 TYR cc_start: 0.1254 (p90) cc_final: 0.0360 (p90) REVERT: I 97 TYR cc_start: 0.1123 (OUTLIER) cc_final: -0.0395 (p90) outliers start: 90 outliers final: 75 residues processed: 296 average time/residue: 0.1996 time to fit residues: 103.8198 Evaluate side-chains 309 residues out of total 4054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 220 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 987 GLN Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 112 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 213 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 385 optimal weight: 9.9990 chunk 97 optimal weight: 0.0060 chunk 132 optimal weight: 0.0870 chunk 463 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 249 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 chunk 203 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 chunk 250 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 GLN ** 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 = 0.4522 r_free = 0.4522 target = 0.146800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.114234 restraints weight = 207209.902| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 7.17 r_work: 0.3470 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 37102 Z= 0.160 Angle : 0.775 59.199 50474 Z= 0.421 Chirality : 0.046 0.333 5675 Planarity : 0.005 0.123 6483 Dihedral : 5.827 56.230 5099 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.61 % Favored : 90.05 % Rotamer: Outliers : 2.22 % Allowed : 17.37 % Favored : 80.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.23 (0.12), residues: 4641 helix: 1.21 (0.20), residues: 726 sheet: 0.02 (0.15), residues: 1233 loop : -1.91 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1074 TYR 0.053 0.002 TYR B 87 PHE 0.031 0.001 PHE B 232 TRP 0.016 0.001 TRP E 35 HIS 0.011 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00335 (37054) covalent geometry : angle 0.77307 (50378) SS BOND : bond 0.00392 ( 48) SS BOND : angle 1.42630 ( 96) hydrogen bonds : bond 0.04263 ( 1200) hydrogen bonds : angle 5.48533 ( 3258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14769.83 seconds wall clock time: 252 minutes 2.35 seconds (15122.35 seconds total)