Starting phenix.real_space_refine on Fri Mar 6 20:52:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6n_31743/03_2026/7v6n_31743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6n_31743/03_2026/7v6n_31743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v6n_31743/03_2026/7v6n_31743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6n_31743/03_2026/7v6n_31743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v6n_31743/03_2026/7v6n_31743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6n_31743/03_2026/7v6n_31743.map" } resolution = 3.99 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 183 5.16 5 C 21700 2.51 5 N 5767 2.21 5 O 6798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.02s 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: 34448 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 8343 Classifications: {'peptide': 1135} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 49, 'TRANS': 1085} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 13, 'HIS:plan': 4, 'GLN:plan1': 10, 'PHE:plan': 14, 'ASN:plan1': 7, 'ARG:plan': 8, 'ASP:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 343 Chain: "B" Number of atoms: 8184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1102, 8178 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 45, 'TRANS': 1056} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 9, 'TYR:plan': 10, 'ASN:plan1': 7, 'GLU:plan': 6, 'PHE:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 282 Conformer: "B" Number of residues, atoms: 1102, 8178 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 45, 'TRANS': 1056} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 9, 'TYR:plan': 10, 'ASN:plan1': 7, 'GLU:plan': 6, 'PHE:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 282 bond proxies already assigned to first conformer: 8337 Chain: "C" Number of atoms: 8029 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1097, 8023 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 48, 'TRANS': 1048} Chain breaks: 12 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'PHE:plan': 13, 'HIS:plan': 6, 'ASN:plan1': 9, 'ARG:plan': 9, 'TYR:plan': 10, 'GLU:plan': 8, 'ASP:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 348 Conformer: "B" Number of residues, atoms: 1097, 8023 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 48, 'TRANS': 1048} Chain breaks: 12 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'PHE:plan': 13, 'HIS:plan': 6, 'ASN:plan1': 9, 'ARG:plan': 9, 'TYR:plan': 10, 'GLU:plan': 8, 'ASP:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 348 bond proxies already assigned to first conformer: 8171 Chain: "D" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1623 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1658 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 215} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1637 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1700 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 215} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1622 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1652 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 215} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1, 'TYR:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 58 Residues with excluded nonbonded symmetry interactions: 2 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: 9.96, per 1000 atoms: 0.29 Number of scatterers: 34448 At special positions: 0 Unit cell: (208.601, 220.678, 203.112, 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 183 16.00 O 6798 8.00 N 5767 7.00 C 21700 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=2.04 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 199 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 156 " - pdb=" SG CYS I 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 2.2 seconds 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8682 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 71 sheets defined 18.7% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.114A pdb=" N SER A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 342 through 350 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 410 through 418 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.848A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.561A pdb=" N ASN A 812 " --> pdb=" O TYR A 809 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 813 " --> pdb=" O VAL A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 813' Processing helix chain 'A' and resid 814 through 823 removed outlier: 4.156A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 852 removed outlier: 4.108A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.265A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 987 through 1011 removed outlier: 3.507A pdb=" N ASN A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1041 Processing helix chain 'A' and resid 1059 through 1106 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.104A 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 410 through 418 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 530 removed outlier: 4.095A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.669A pdb=" N TYR B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 854 removed outlier: 3.881A pdb=" N VAL B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 915 Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 955 through 958 removed outlier: 3.768A pdb=" N VAL B 958 " --> pdb=" O ILE B 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 955 through 958' Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 987 through 994 Processing helix chain 'B' and resid 996 through 1010 Processing helix chain 'B' and resid 1017 through 1041 removed outlier: 3.777A pdb=" N LYS B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1106 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.640A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 268 through 273 removed outlier: 4.182A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 410 through 418 Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.691A pdb=" N SER C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 824 through 854 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 915 Processing helix chain 'C' and resid 925 through 930 Processing helix chain 'C' and resid 940 through 958 Processing helix chain 'C' and resid 975 through 982 Processing helix chain 'C' and resid 1005 through 1011 Processing helix chain 'C' and resid 1018 through 1041 removed outlier: 3.576A pdb=" N VAL C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1106 Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 144 through 149 removed outlier: 3.560A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.547A pdb=" N LEU F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 Processing helix chain 'G' and resid 144 through 149 removed outlier: 3.680A pdb=" N SER G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 188 through 194 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 144 through 149 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.679A pdb=" N VAL A 102 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 75 removed outlier: 3.543A pdb=" N GLY A 73 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.783A pdb=" N TYR A 314 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 119 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 243 removed outlier: 7.615A pdb=" N ARG A 235 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU A 188 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS A 237 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE A 186 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 239 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 184 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 206 through 208 removed outlier: 5.365A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 367 removed outlier: 5.490A pdb=" N SER A 362 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL A 661 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER A 364 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL A 659 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 671 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 400 through 404 removed outlier: 7.230A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.343A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 605 through 607 removed outlier: 3.858A pdb=" N GLY A 613 " --> pdb=" O TYR A 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 631 through 632 Processing sheet with id=AB3, first strand: chain 'A' and resid 779 through 781 Processing sheet with id=AB4, first strand: chain 'A' and resid 801 through 803 removed outlier: 4.585A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1121 through 1128 removed outlier: 5.555A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.579A pdb=" N LEU B 325 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 73 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.676A pdb=" N ILE B 120 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 252 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.564A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.282A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.282A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.543A pdb=" N GLY B 128 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 138 " --> pdb=" O GLY B 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.829A pdb=" N TYR B 361 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 661 " --> pdb=" O TYR B 361 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 662 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 671 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 375 through 376 removed outlier: 3.676A pdb=" N GLU B 376 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 400 through 405 removed outlier: 3.578A pdb=" N LYS B 400 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.161A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 631 through 632 Processing sheet with id=AC9, first strand: chain 'B' and resid 791 through 795 removed outlier: 3.614A pdb=" N THR B 791 " --> pdb=" O HIS B1138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD2, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AD3, first strand: chain 'C' and resid 69 through 76 removed outlier: 3.694A pdb=" N ILE C 69 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.644A pdb=" N LEU C 324 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AD6, first strand: chain 'C' and resid 232 through 244 removed outlier: 4.556A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS C 185 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.554A pdb=" N ARG C 163 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 206 through 208 removed outlier: 5.491A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 359 through 367 removed outlier: 4.633A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 672 " --> pdb=" O ASN C 719 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 400 through 405 removed outlier: 3.639A pdb=" N LYS C 400 " --> pdb=" O TYR C 445 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AE3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.061A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 777 through 783 removed outlier: 3.507A pdb=" N LEU C 780 " --> pdb=" O VAL C1149 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AE6, first strand: chain 'C' and resid 1127 through 1130 Processing sheet with id=AE7, first strand: chain 'D' and resid 14 through 15 removed outlier: 6.161A pdb=" N LEU D 14 " --> pdb=" O GLU D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 22 through 27 Processing sheet with id=AE9, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.571A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR D 35 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 119 through 123 Processing sheet with id=AF2, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AF3, first strand: chain 'D' and resid 158 through 160 removed outlier: 4.508A pdb=" N TRP D 153 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.336A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.251A pdb=" N GLY E 155 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA E 152 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR E 192 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER E 193 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA E 184 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER E 195 " --> pdb=" O PHE E 182 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.629A pdb=" N THR E 221 " --> pdb=" O HIS E 216 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 13 through 15 Processing sheet with id=AF9, first strand: chain 'F' and resid 22 through 26 Processing sheet with id=AG1, first strand: chain 'F' and resid 48 through 51 removed outlier: 6.640A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 119 through 123 Processing sheet with id=AG3, first strand: chain 'F' and resid 158 through 160 removed outlier: 4.413A pdb=" N TRP F 153 " --> pdb=" O GLN F 160 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.782A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 58 through 60 removed outlier: 5.370A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 136 through 140 removed outlier: 3.783A pdb=" N GLY G 155 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA G 152 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP G 160 " --> pdb=" O TYR G 192 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR G 192 " --> pdb=" O ASP G 160 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AG8, first strand: chain 'H' and resid 8 through 9 removed outlier: 4.210A pdb=" N THR H 8 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 13 through 15 Processing sheet with id=AH1, first strand: chain 'H' and resid 48 through 51 removed outlier: 6.608A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR H 88 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 119 through 123 Processing sheet with id=AH3, first strand: chain 'H' and resid 134 through 135 Processing sheet with id=AH4, first strand: chain 'H' and resid 158 through 160 removed outlier: 4.554A pdb=" N TRP H 153 " --> pdb=" O GLN H 160 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.647A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.406A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 136 through 140 removed outlier: 4.313A pdb=" N GLY I 155 " --> pdb=" O LEU I 140 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP I 160 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR I 192 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 166 through 170 1227 hydrogen bonds defined for protein. 3312 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: 7.63 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6638 1.33 - 1.45: 8722 1.45 - 1.58: 19566 1.58 - 1.70: 0 1.70 - 1.82: 233 Bond restraints: 35159 Sorted by residual: bond pdb=" N VAL A 657 " pdb=" CA VAL A 657 " ideal model delta sigma weight residual 1.460 1.497 -0.036 7.60e-03 1.73e+04 2.30e+01 bond pdb=" N ARG I 87 " pdb=" CA ARG I 87 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.89e+01 bond pdb=" N CYS B 195 " pdb=" CA CYS B 195 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.80e+01 bond pdb=" N ILE B 296 " pdb=" CA ILE B 296 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.50e-03 1.78e+04 1.76e+01 bond pdb=" N ILE C 782 " pdb=" CA ILE C 782 " ideal model delta sigma weight residual 1.457 1.495 -0.037 9.00e-03 1.23e+04 1.73e+01 ... (remaining 35154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 45052 2.86 - 5.73: 2814 5.73 - 8.59: 60 8.59 - 11.46: 5 11.46 - 14.32: 1 Bond angle restraints: 47932 Sorted by residual: angle pdb=" C ASP B 510 " pdb=" CA ASP B 510 " pdb=" CB ASP B 510 " ideal model delta sigma weight residual 109.83 117.39 -7.56 9.90e-01 1.02e+00 5.83e+01 angle pdb=" N LEU B 600 " pdb=" CA LEU B 600 " pdb=" C LEU B 600 " ideal model delta sigma weight residual 114.56 105.99 8.57 1.27e+00 6.20e-01 4.55e+01 angle pdb=" N ALA B 930 " pdb=" CA ALA B 930 " pdb=" C ALA B 930 " ideal model delta sigma weight residual 110.80 96.48 14.32 2.13e+00 2.20e-01 4.52e+01 angle pdb=" N CYS A 603 " pdb=" CA CYS A 603 " pdb=" C CYS A 603 " ideal model delta sigma weight residual 108.41 118.37 -9.96 1.63e+00 3.76e-01 3.74e+01 angle pdb=" N ARG H 147 " pdb=" CA ARG H 147 " pdb=" C ARG H 147 " ideal model delta sigma weight residual 111.36 104.76 6.60 1.09e+00 8.42e-01 3.67e+01 ... (remaining 47927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 19005 16.83 - 33.67: 1345 33.67 - 50.50: 478 50.50 - 67.33: 120 67.33 - 84.17: 12 Dihedral angle restraints: 20960 sinusoidal: 7425 harmonic: 13535 Sorted by residual: dihedral pdb=" CB CYS F 26 " pdb=" SG CYS F 26 " pdb=" SG CYS F 91 " pdb=" CB CYS F 91 " ideal model delta sinusoidal sigma weight residual -86.00 -170.17 84.17 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS C 679 " pdb=" SG CYS C 679 " pdb=" SG CYS C 713 " pdb=" CB CYS C 713 " ideal model delta sinusoidal sigma weight residual -86.00 -157.98 71.98 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 620 " pdb=" SG CYS A 620 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual -86.00 -150.59 64.59 1 1.00e+01 1.00e-02 5.48e+01 ... (remaining 20957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3861 0.115 - 0.230: 1585 0.230 - 0.346: 101 0.346 - 0.461: 1 0.461 - 0.576: 2 Chirality restraints: 5550 Sorted by residual: chirality pdb=" CA ARG B1179 " pdb=" N ARG B1179 " pdb=" C ARG B1179 " pdb=" CB ARG B1179 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.29e+00 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 2.01 0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CA ASN F 143 " pdb=" N ASN F 143 " pdb=" C ASN F 143 " pdb=" CB ASN F 143 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 5547 not shown) Planarity restraints: 6205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BSER C 51 " -0.034 2.00e-02 2.50e+03 7.10e-02 5.04e+01 pdb=" C BSER C 51 " 0.123 2.00e-02 2.50e+03 pdb=" O BSER C 51 " -0.046 2.00e-02 2.50e+03 pdb=" N LYS C 52 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASER C 51 " -0.031 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C ASER C 51 " 0.110 2.00e-02 2.50e+03 pdb=" O ASER C 51 " -0.041 2.00e-02 2.50e+03 pdb=" N LYS C 52 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 50 " 0.030 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C VAL B 50 " -0.106 2.00e-02 2.50e+03 pdb=" O VAL B 50 " 0.039 2.00e-02 2.50e+03 pdb=" N BSER B 51 " 0.037 2.00e-02 2.50e+03 ... (remaining 6202 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 7 1.96 - 2.70: 886 2.70 - 3.43: 47148 3.43 - 4.17: 85730 4.17 - 4.90: 141178 Nonbonded interactions: 274949 Sorted by model distance: nonbonded pdb=" CB LYS A 42 " pdb=" CZ3 TRP A 44 " model vdw 1.225 3.740 nonbonded pdb=" O ALA A 520 " pdb=" OD1 ASN A 521 " model vdw 1.282 3.040 nonbonded pdb=" CB LYS A 42 " pdb=" CH2 TRP A 44 " model vdw 1.306 3.740 nonbonded pdb=" OG SER B 328 " pdb=" CG ARG B 334 " model vdw 1.536 3.440 nonbonded pdb=" OD2 ASP B 330 " pdb=" NH2 ARG B 334 " model vdw 1.788 3.120 ... (remaining 274944 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 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and ( \ name N or name CA or name C or name O or name CB )) or resid 45 or (resid 46 and \ (name N or name CA or name C or name O or name CB )) or resid 47 or (resid 48 t \ hrough 49 and (name N or name CA or name C or name O or name CB )) or resid 50 o \ r (resid 52 through 54 and (name N or name CA or name C or name O or name CB )) \ or resid 55 through 59 or (resid 60 and (name N or name CA or name C or name O o \ r name CB )) or resid 61 or (resid 62 through 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 through 83 or (resid 84 and (name N or nam \ e CA or name C or name O or name CB )) or resid 85 through 87 or (resid 88 throu \ gh 89 and (name N or name CA or name C or name O or name CB )) or resid 90 throu \ gh 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or r \ esid 100 through 103 or (resid 104 and (name N or name CA or name C or name O or \ name CB )) or resid 105 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 118 or (resid 119 a \ nd (name N or name CA or name C or name O or name CB )) or resid 120 through 130 \ or (resid 131 and (name N or name CA or name C or name O or name CB )) or resid \ 132 through 180 or (resid 181 through 182 and (name N or name CA or name C or n \ ame O or name CB )) or resid 183 through 189 or (resid 190 and (name N or name C \ A or name C or name O or name CB )) or resid 191 through 192 or (resid 193 throu \ gh 194 and (name N or name CA or name C or name O or name CB )) or resid 195 thr \ ough 199 or (resid 200 through 201 and (name N or name CA or name C or name O or \ name CB )) or resid 202 through 206 or (resid 207 through 208 and (name N or na \ me CA or name C or name O or name CB )) or resid 209 through 220 or (resid 221 a \ nd (name N or name CA or name C or name O or name CB )) or resid 222 through 229 \ or (resid 230 through 231 and (name N or name CA or name C or name O or name CB \ )) or resid 232 through 257 or (resid 258 and (name N or name CA or name C or n \ ame O or name CB )) or resid 259 through 260 or (resid 261 and (name N or name C \ A or name C or name O or name CB )) or resid 262 through 290 or (resid 291 and ( \ name N or name CA or name C or name O or name CB )) or resid 292 through 300 or \ (resid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 \ through 313 or (resid 314 and (name N or name CA or name C or name O or name CB \ )) or resid 315 through 357 or (resid 358 and (name N or name CA or name C or n \ ame O or name CB )) or resid 359 through 362 or (resid 363 and (name N or name 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(resid 910 and (name N or name CA or name C or name O or name \ CB )) or resid 911 through 912 or (resid 913 and (name N or name CA or name C o \ r name O or name CB )) or resid 914 through 927 or (resid 928 and (name N or nam \ e CA or name C or name O or name CB )) or resid 929 through 946 or (resid 947 an \ d (name N or name CA or name C or name O or name CB )) or resid 948 through 958 \ or (resid 972 through 974 and (name N or name CA or name C or name O or name CB \ )) or resid 975 or (resid 976 through 979 and (name N or name CA or name C or na \ me O or name CB )) or resid 980 through 1007 or (resid 1008 through 1009 and (na \ me N or name CA or name C or name O or name CB )) or resid 1010 through 1011 or \ (resid 1012 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 13 through 1019 or (resid 1020 through 1021 and (name N or name CA or name C or \ name O or name CB )) or resid 1022 through 1042 or (resid 1043 through 1044 and \ (name N or name CA or name C or name O or name CB )) or resid 1045 through 1049 \ or (resid 1050 and (name N or name CA or name C or name O or name CB )) or resid \ 1051 through 1052 or (resid 1053 and (name N or name CA or name C or name O or \ name CB )) or resid 1054 or (resid 1055 through 1059 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1060 through 1061 or (resid 1062 through \ 1066 and (name N or name CA or name C or name O or name CB )) or resid 1067 or ( \ resid 1068 and (name N or name CA or name C or name O or name CB )) or resid 106 \ 9 through 1120 or (resid 1122 and (name N or name CA or name C or name O or name \ CB )) or resid 1123 through 1136 or (resid 1137 and (name N or name CA or name \ C or name O or name CB )) or resid 1138 through 1148 or (resid 1149 and (name N \ or name CA or name C or name O or name CB )) or resid 1150 through 1156 or resid \ 1164 through 1188)) } ncs_group { reference = (chain 'D' and (resid 4 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 122 or (resid 123 and (name N or na \ me CA or name C or name O or name CB )) or resid 124 through 137 or (resid 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 151 \ or (resid 152 and (name N or name CA or name C or name O or name CB )) or resid \ 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or r \ esid 155 through 175 or (resid 176 through 177 and (name N or name CA or name C \ or name O or name CB )) or resid 178 through 199 or (resid 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 219)) selection = (chain 'F' and (resid 4 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB )) or resid 75 through 127 or (resid 128 through 129 and ( \ name N or name CA or name C or name O or name CB )) or resid 130 through 142 or \ (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 \ through 151 or (resid 152 and (name N or name CA or name C or name O or name CB \ )) or resid 153 or (resid 154 and (name N or name CA or name C or name O or nam \ e CB )) or resid 155 through 174 or (resid 175 through 177 and (name N or name C \ A or name C or name O or name CB )) or resid 178 through 199 or (resid 200 and ( \ name N or name CA or name C or name O or name CB )) or resid 201 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 \ )) selection = (chain 'H' and (resid 4 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 127 or (resid 128 through 129 and ( \ name N or name CA or name C or name O or name CB )) or resid 130 through 142 or \ (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 \ through 174 or (resid 175 through 177 and (name N or name CA or name C or name \ O or name CB )) or resid 178 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219)) } ncs_group { reference = (chain 'E' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 56 or (resid 57 through 61 and (nam \ e N or name CA or name C or name O or name CB )) or resid 62 through 78 or (resi \ d 79 and (name N or name CA or name C or name O or name CB )) or resid 80 throug \ h 102 or (resid 103 through 104 and (name N or name CA or name C or name O or na \ me CB )) or resid 105 through 106 or (resid 107 and (name N or name CA or name C \ or name O or name CB )) or resid 108 through 109 or (resid 110 and (name N or n \ ame CA or name C or name O or name CB )) or resid 111 through 160 or (resid 161 \ through 162 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 3 through 165 or (resid 166 and (name N or name CA or name C or name O or name C \ B )) or resid 167 through 227)) selection = (chain 'G' and (resid 1 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 51 or (resid 52 through \ 54 and (name N or name CA or name C or name O or name CB )) or resid 55 through \ 56 or (resid 57 through 61 and (name N or name CA or name C or name O or name CB \ )) or resid 62 through 97 or (resid 98 and (name N or name CA or name C or name \ O or name CB )) or resid 99 through 102 or (resid 103 through 104 and (name N o \ r name CA or name C or name O or name CB )) or resid 105 through 106 or (resid 1 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 108 through \ 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or r \ esid 111 through 115 or (resid 116 and (name N or name CA or name C or name O or \ name CB )) or resid 117 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 160 or (resid 1 \ 61 through 162 and (name N or name CA or name C or name O or name CB )) or resid \ 163 through 165 or (resid 166 and (name N or name CA or name C or name O or nam \ e CB )) or resid 167 through 227)) selection = (chain 'I' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 78 or (resid 79 and (nam \ e N or name CA or name C or name O or name CB )) or resid 80 through 97 or (resi \ d 98 and (name N or name CA or name C or name O or name CB )) or resid 99 throug \ h 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) or \ resid 117 through 132 or (resid 133 and (name N or name CA or name C or name O o \ r name CB )) or resid 134 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 142 or (resid 143 and (name N \ or name CA or name C or name O or name CB )) or resid 144 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throug \ h 227)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.380 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4839 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 : 0.013 0.064 35207 Z= 1.016 Angle : 1.540 14.320 48028 Z= 1.182 Chirality : 0.106 0.576 5550 Planarity : 0.004 0.071 6205 Dihedral : 13.593 82.266 12134 Min Nonbonded Distance : 1.225 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 1.13 % Allowed : 3.97 % Favored : 94.90 % Rotamer: Outliers : 8.11 % Allowed : 10.19 % Favored : 81.71 % Cbeta Deviations : 0.51 % 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: 1.46 (0.12), residues: 4595 helix: 4.29 (0.18), residues: 721 sheet: 1.94 (0.15), residues: 1174 loop : -0.46 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 758 TYR 0.031 0.002 TYR A 314 PHE 0.017 0.002 PHE A1116 TRP 0.013 0.001 TRP E 120 HIS 0.006 0.001 HIS C1122 Details of bonding type rmsd covalent geometry : bond 0.01322 (35159) covalent geometry : angle 1.54008 (47932) SS BOND : bond 0.00490 ( 48) SS BOND : angle 1.45102 ( 96) hydrogen bonds : bond 0.19569 ( 1208) hydrogen bonds : angle 7.91699 ( 3312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 502 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.6629 (t80) REVERT: A 424 THR cc_start: 0.2110 (OUTLIER) cc_final: 0.1896 (p) REVERT: A 795 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.6910 (mm) REVERT: A 799 ILE cc_start: 0.7978 (pt) cc_final: 0.7517 (pt) REVERT: A 903 PRO cc_start: 0.0716 (Cg_endo) cc_final: 0.0383 (Cg_exo) REVERT: A 1061 LEU cc_start: 0.3764 (OUTLIER) cc_final: 0.3559 (tp) REVERT: A 1127 VAL cc_start: 0.7551 (t) cc_final: 0.7339 (m) REVERT: A 1149 VAL cc_start: 0.4306 (OUTLIER) cc_final: 0.4075 (t) REVERT: B 400 LYS cc_start: 0.7169 (tptm) cc_final: 0.6842 (ttpt) REVERT: B 433 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.4275 (pt) REVERT: B 477 THR cc_start: 0.0238 (OUTLIER) cc_final: -0.0073 (p) REVERT: B 620 CYS cc_start: 0.3455 (OUTLIER) cc_final: 0.2894 (m) REVERT: B 667 THR cc_start: 0.6428 (p) cc_final: 0.6207 (p) REVERT: B 696 MET cc_start: 0.6594 (ppp) cc_final: 0.6110 (ptm) REVERT: B 970 ILE cc_start: 0.4782 (OUTLIER) cc_final: 0.4572 (tt) REVERT: B 983 VAL cc_start: 0.5647 (OUTLIER) cc_final: 0.4215 (m) REVERT: B 989 VAL cc_start: 0.6814 (OUTLIER) cc_final: 0.6180 (p) REVERT: C 393 PRO cc_start: 0.4528 (Cg_exo) cc_final: 0.4293 (Cg_endo) REVERT: C 395 GLN cc_start: 0.4649 (mm-40) cc_final: 0.4382 (mm-40) REVERT: C 401 ARG cc_start: 0.2987 (OUTLIER) cc_final: 0.2424 (ptp-110) REVERT: C 473 PHE cc_start: 0.4220 (p90) cc_final: 0.3981 (p90) REVERT: C 523 TYR cc_start: 0.3815 (m-80) cc_final: 0.3294 (m-10) REVERT: C 606 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.4900 (p90) REVERT: C 639 VAL cc_start: 0.3151 (OUTLIER) cc_final: 0.2707 (t) REVERT: C 651 LEU cc_start: 0.6874 (mt) cc_final: 0.6197 (mt) REVERT: C 938 LEU cc_start: 0.4710 (OUTLIER) cc_final: 0.4483 (tp) REVERT: C 1040 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5477 (mt) REVERT: C 1086 LEU cc_start: 0.8236 (mt) cc_final: 0.7961 (tp) REVERT: D 52 TYR cc_start: 0.3886 (t80) cc_final: 0.2288 (t80) REVERT: D 181 SER cc_start: -0.0051 (OUTLIER) cc_final: -0.0256 (t) REVERT: D 186 LEU cc_start: 0.0456 (OUTLIER) cc_final: -0.0048 (tp) REVERT: E 68 PHE cc_start: 0.3515 (m-10) cc_final: 0.3090 (m-80) REVERT: E 83 MET cc_start: 0.4544 (mtm) cc_final: 0.4154 (mpp) REVERT: E 186 LEU cc_start: 0.3263 (OUTLIER) cc_final: 0.2972 (mm) REVERT: F 6 GLN cc_start: 0.5327 (OUTLIER) cc_final: 0.4986 (mp10) REVERT: F 7 MET cc_start: 0.4020 (tmm) cc_final: 0.3335 (tmm) REVERT: F 36 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5063 (mm) REVERT: F 75 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7355 (m) REVERT: F 122 ILE cc_start: 0.1688 (tp) cc_final: 0.1471 (tp) REVERT: G 83 MET cc_start: 0.4753 (mtm) cc_final: 0.4310 (mpp) REVERT: G 166 VAL cc_start: -0.1241 (OUTLIER) cc_final: -0.1556 (p) REVERT: G 168 VAL cc_start: 0.1191 (OUTLIER) cc_final: 0.0503 (p) REVERT: G 191 LEU cc_start: 0.2287 (OUTLIER) cc_final: 0.1986 (mp) REVERT: H 51 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3399 (tt) REVERT: H 86 PHE cc_start: 0.4766 (m-10) cc_final: 0.4553 (m-10) REVERT: H 112 LYS cc_start: 0.5651 (mtmm) cc_final: 0.5427 (mttp) REVERT: I 48 VAL cc_start: 0.6597 (OUTLIER) cc_final: 0.6366 (p) REVERT: I 93 VAL cc_start: 0.4254 (OUTLIER) cc_final: 0.3993 (p) REVERT: I 95 TYR cc_start: 0.5023 (m-80) cc_final: 0.4428 (m-80) REVERT: I 194 LEU cc_start: -0.0297 (OUTLIER) cc_final: -0.0505 (pp) outliers start: 296 outliers final: 53 residues processed: 750 average time/residue: 0.1959 time to fit residues: 245.2817 Evaluate side-chains 333 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 251 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 161 TYR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 200 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.1980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 280 GLN A 516 GLN A 522 GLN A 566 GLN A 627 GLN A 733 GLN A 765 ASN A 785 ASN A 848 ASN A 999 ASN A1020 GLN A1084 GLN A1146 HIS A1163 ASN B 114 ASN B 319 GLN B 346 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN B 833 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN B1110 GLN B1129 ASN C 72 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 226 ASN C 277 ASN C 280 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN C 522 GLN C 618 GLN C 733 GLN C 832 ASN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1129 ASN C1160 ASN C1176 ASN C1177 ASN D 160 GLN D 171 GLN E 31 ASN E 35 HIS ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 122 GLN G 187 GLN H 93 GLN H 129 GLN H 160 GLN H 171 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.109111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.095227 restraints weight = 256859.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.088275 restraints weight = 294493.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.083956 restraints weight = 298424.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.083815 restraints weight = 264428.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.083792 restraints weight = 200750.425| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35207 Z= 0.152 Angle : 0.680 10.798 48028 Z= 0.362 Chirality : 0.044 0.233 5550 Planarity : 0.004 0.056 6205 Dihedral : 6.685 57.200 5109 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.33 % Favored : 96.30 % Rotamer: Outliers : 4.35 % Allowed : 14.38 % Favored : 81.27 % 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: 0.64 (0.12), residues: 4595 helix: 2.47 (0.18), residues: 762 sheet: 1.58 (0.15), residues: 1182 loop : -0.80 (0.11), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 841 TYR 0.054 0.002 TYR A 909 PHE 0.039 0.002 PHE A 281 TRP 0.030 0.002 TRP A 44 HIS 0.011 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00318 (35159) covalent geometry : angle 0.67798 (47932) SS BOND : bond 0.00268 ( 48) SS BOND : angle 1.38077 ( 96) hydrogen bonds : bond 0.06182 ( 1208) hydrogen bonds : angle 6.33428 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 272 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6341 (mtpt) REVERT: A 795 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7441 (mt) REVERT: A 952 LEU cc_start: 0.8407 (tp) cc_final: 0.8187 (mt) REVERT: A 1061 LEU cc_start: 0.3791 (OUTLIER) cc_final: 0.3548 (tt) REVERT: A 1127 VAL cc_start: 0.8399 (t) cc_final: 0.8198 (m) REVERT: A 1149 VAL cc_start: 0.5562 (OUTLIER) cc_final: 0.5315 (t) REVERT: A 1179 ARG cc_start: 0.8058 (tmm-80) cc_final: 0.7796 (tmm-80) REVERT: B 333 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6665 (mt) REVERT: B 477 THR cc_start: -0.0920 (OUTLIER) cc_final: -0.1205 (p) REVERT: B 565 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5382 (pm20) REVERT: B 620 CYS cc_start: 0.4362 (OUTLIER) cc_final: 0.3680 (m) REVERT: B 696 MET cc_start: 0.7078 (ppp) cc_final: 0.6782 (ptm) REVERT: C 171 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7401 (pt) REVERT: C 397 TYR cc_start: 0.3554 (p90) cc_final: 0.2866 (p90) REVERT: C 609 TYR cc_start: 0.2941 (OUTLIER) cc_final: 0.2486 (m-80) REVERT: C 819 GLN cc_start: 0.6434 (mt0) cc_final: 0.6136 (mm-40) REVERT: C 906 MET cc_start: 0.0586 (mmp) cc_final: 0.0200 (mmp) REVERT: D 52 TYR cc_start: 0.5134 (t80) cc_final: 0.3362 (t80) REVERT: D 105 GLN cc_start: 0.5609 (mm-40) cc_final: 0.5305 (tt0) REVERT: E 68 PHE cc_start: 0.3982 (m-10) cc_final: 0.3696 (m-80) REVERT: E 83 MET cc_start: 0.4645 (mtm) cc_final: 0.3712 (mpp) REVERT: F 6 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.5072 (mp10) REVERT: F 36 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6357 (mm) REVERT: F 92 GLN cc_start: 0.3399 (OUTLIER) cc_final: 0.2265 (mp10) REVERT: F 112 LYS cc_start: 0.6474 (mtmm) cc_final: 0.6091 (mmmt) REVERT: G 83 MET cc_start: 0.5025 (mtm) cc_final: 0.3830 (mpp) REVERT: G 166 VAL cc_start: 0.2800 (OUTLIER) cc_final: 0.2554 (p) REVERT: I 6 GLU cc_start: 0.3422 (OUTLIER) cc_final: 0.2948 (mm-30) REVERT: I 95 TYR cc_start: 0.5433 (m-80) cc_final: 0.5092 (m-80) outliers start: 159 outliers final: 76 residues processed: 411 average time/residue: 0.1920 time to fit residues: 133.8427 Evaluate side-chains 291 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 200 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 SER Chi-restraints excluded: chain C residue 1156 CYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 161 TYR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 410 optimal weight: 50.0000 chunk 384 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 453 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 371 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 144 optimal weight: 0.0870 chunk 223 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 2.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN A 733 GLN A 785 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN B 681 HIS B 765 ASN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 815 GLN C 839 ASN C 907 GLN C1023 GLN C1042 ASN C1138 HIS D 6 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN G 82 GLN ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 HIS ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.106979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.079030 restraints weight = 329938.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.076693 restraints weight = 301901.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.075951 restraints weight = 405841.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.076159 restraints weight = 326496.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.076371 restraints weight = 273167.721| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 35207 Z= 0.158 Angle : 0.661 14.603 48028 Z= 0.349 Chirality : 0.044 0.296 5550 Planarity : 0.005 0.081 6205 Dihedral : 5.905 57.799 5044 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.55 % Favored : 95.10 % Rotamer: Outliers : 3.97 % Allowed : 15.25 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4595 helix: 1.88 (0.19), residues: 774 sheet: 1.24 (0.15), residues: 1166 loop : -0.98 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 694 TYR 0.031 0.002 TYR E 192 PHE 0.024 0.002 PHE A 617 TRP 0.034 0.002 TRP C 553 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00340 (35159) covalent geometry : angle 0.65566 (47932) SS BOND : bond 0.00524 ( 48) SS BOND : angle 1.96883 ( 96) hydrogen bonds : bond 0.05409 ( 1208) hydrogen bonds : angle 5.89350 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 219 time to evaluate : 1.260 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: A 795 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7872 (mm) REVERT: A 1036 LEU cc_start: 0.8112 (mt) cc_final: 0.7895 (mp) REVERT: B 620 CYS cc_start: 0.4196 (OUTLIER) cc_final: 0.3678 (m) REVERT: C 397 TYR cc_start: 0.3543 (p90) cc_final: 0.3163 (p90) REVERT: C 819 GLN cc_start: 0.6795 (mt0) cc_final: 0.6420 (mm-40) REVERT: D 52 TYR cc_start: 0.5339 (t80) cc_final: 0.4020 (t80) REVERT: F 92 GLN cc_start: 0.3731 (OUTLIER) cc_final: 0.2546 (mp10) REVERT: G 83 MET cc_start: 0.5445 (mtm) cc_final: 0.5171 (mpp) outliers start: 145 outliers final: 94 residues processed: 350 average time/residue: 0.1941 time to fit residues: 114.5775 Evaluate side-chains 288 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 191 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 797 THR Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 809 TYR Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain C residue 1156 CYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 260 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 445 optimal weight: 9.9990 chunk 202 optimal weight: 0.1980 chunk 360 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 386 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 455 optimal weight: 9.9990 chunk 458 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 319 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN D 171 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.106621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.080254 restraints weight = 414840.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.076925 restraints weight = 390421.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.076695 restraints weight = 499913.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.076229 restraints weight = 425446.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.076462 restraints weight = 321142.165| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3908 r_free = 0.3908 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3908 r_free = 0.3908 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35207 Z= 0.131 Angle : 0.606 9.501 48028 Z= 0.319 Chirality : 0.043 0.224 5550 Planarity : 0.004 0.059 6205 Dihedral : 5.622 59.701 5031 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.36 % Favored : 95.36 % Rotamer: Outliers : 3.50 % Allowed : 16.02 % Favored : 80.48 % 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: 0.07 (0.12), residues: 4595 helix: 1.80 (0.19), residues: 783 sheet: 1.13 (0.15), residues: 1172 loop : -1.06 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1179 TYR 0.033 0.002 TYR C 438 PHE 0.035 0.002 PHE C1044 TRP 0.030 0.001 TRP E 111 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00272 (35159) covalent geometry : angle 0.60375 (47932) SS BOND : bond 0.00265 ( 48) SS BOND : angle 1.23318 ( 96) hydrogen bonds : bond 0.04866 ( 1208) hydrogen bonds : angle 5.64748 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 201 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 TYR cc_start: 0.2811 (p90) cc_final: 0.2592 (p90) REVERT: A 549 GLU cc_start: 0.3150 (OUTLIER) cc_final: 0.2896 (tp30) REVERT: A 795 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7771 (mm) REVERT: B 104 ASN cc_start: 0.5056 (OUTLIER) cc_final: 0.4667 (t0) REVERT: B 620 CYS cc_start: 0.3007 (OUTLIER) cc_final: 0.2578 (m) REVERT: C 77 TYR cc_start: 0.5389 (p90) cc_final: 0.5174 (p90) REVERT: C 397 TYR cc_start: 0.3635 (p90) cc_final: 0.3389 (p90) REVERT: C 819 GLN cc_start: 0.6523 (mt0) cc_final: 0.6196 (mm-40) REVERT: C 827 PHE cc_start: 0.6161 (m-80) cc_final: 0.5834 (m-80) REVERT: C 906 MET cc_start: 0.1010 (mmp) cc_final: 0.0225 (mmp) REVERT: C 1043 THR cc_start: 0.7106 (p) cc_final: 0.6852 (t) REVERT: D 52 TYR cc_start: 0.5379 (t80) cc_final: 0.4582 (t80) REVERT: D 181 SER cc_start: 0.2028 (OUTLIER) cc_final: 0.1824 (t) REVERT: F 6 GLN cc_start: 0.6715 (pp30) cc_final: 0.6477 (mp10) REVERT: F 92 GLN cc_start: 0.3779 (OUTLIER) cc_final: 0.2665 (mp10) REVERT: G 83 MET cc_start: 0.5285 (mtm) cc_final: 0.4956 (mpp) outliers start: 128 outliers final: 86 residues processed: 320 average time/residue: 0.1938 time to fit residues: 105.3054 Evaluate side-chains 273 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 181 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 341 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 343 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN B 104 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN D 171 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN H 142 ASN H 160 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.104362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.076963 restraints weight = 351717.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.072762 restraints weight = 371421.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.072638 restraints weight = 475261.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.072658 restraints weight = 330386.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.072546 restraints weight = 263030.492| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 35207 Z= 0.171 Angle : 0.665 9.669 48028 Z= 0.352 Chirality : 0.044 0.280 5550 Planarity : 0.005 0.064 6205 Dihedral : 5.825 56.571 5021 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.40 % Favored : 94.33 % Rotamer: Outliers : 3.97 % Allowed : 16.07 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.12), residues: 4595 helix: 1.41 (0.19), residues: 772 sheet: 0.72 (0.15), residues: 1214 loop : -1.25 (0.11), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 401 TYR 0.028 0.002 TYR C 641 PHE 0.033 0.002 PHE C1136 TRP 0.024 0.001 TRP C 553 HIS 0.014 0.002 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00375 (35159) covalent geometry : angle 0.66304 (47932) SS BOND : bond 0.00414 ( 48) SS BOND : angle 1.27156 ( 96) hydrogen bonds : bond 0.04937 ( 1208) hydrogen bonds : angle 5.74270 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 213 time to evaluate : 1.326 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: A 84 MET cc_start: 0.5957 (tpp) cc_final: 0.5675 (mmm) REVERT: A 228 PHE cc_start: 0.7600 (t80) cc_final: 0.7302 (t80) REVERT: A 397 TYR cc_start: 0.3234 (p90) cc_final: 0.2739 (p90) REVERT: A 549 GLU cc_start: 0.3080 (OUTLIER) cc_final: 0.2787 (tp30) REVERT: A 757 MET cc_start: 0.6431 (tpt) cc_final: 0.6039 (ttm) REVERT: A 795 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8048 (mm) REVERT: A 1012 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7176 (t80) REVERT: B 161 MET cc_start: 0.6143 (tmm) cc_final: 0.5817 (tmm) REVERT: B 183 PHE cc_start: 0.4782 (p90) cc_final: 0.3517 (p90) REVERT: B 240 MET cc_start: 0.3920 (mpp) cc_final: 0.3630 (mpp) REVERT: B 620 CYS cc_start: 0.3228 (OUTLIER) cc_final: 0.2816 (m) REVERT: B 662 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5416 (tp) REVERT: C 397 TYR cc_start: 0.3363 (p90) cc_final: 0.3068 (p90) REVERT: C 1137 MET cc_start: 0.7352 (mpp) cc_final: 0.6819 (mpp) REVERT: D 52 TYR cc_start: 0.5305 (t80) cc_final: 0.4611 (t80) REVERT: F 6 GLN cc_start: 0.6815 (pp30) cc_final: 0.6586 (mp10) REVERT: G 83 MET cc_start: 0.5154 (mtm) cc_final: 0.4798 (mpp) outliers start: 145 outliers final: 100 residues processed: 344 average time/residue: 0.1922 time to fit residues: 112.4268 Evaluate side-chains 282 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 177 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1156 CYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 374 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 15 optimal weight: 7.9990 chunk 189 optimal weight: 0.1980 chunk 271 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 361 optimal weight: 10.0000 chunk 373 optimal weight: 20.0000 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 ASN ** I 35 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 = 0.4406 r_free = 0.4406 target = 0.104661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.076793 restraints weight = 331667.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.073088 restraints weight = 321372.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.072917 restraints weight = 399073.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.072928 restraints weight = 285725.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.073006 restraints weight = 238748.605| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 35207 Z= 0.121 Angle : 0.599 11.016 48028 Z= 0.313 Chirality : 0.042 0.189 5550 Planarity : 0.004 0.046 6205 Dihedral : 5.513 57.153 5016 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.92 % Favored : 94.81 % Rotamer: Outliers : 2.98 % Allowed : 17.36 % Favored : 79.65 % 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: -0.28 (0.12), residues: 4595 helix: 1.64 (0.19), residues: 775 sheet: 0.72 (0.15), residues: 1205 loop : -1.25 (0.11), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 56 TYR 0.027 0.002 TYR C 641 PHE 0.021 0.002 PHE B 266 TRP 0.024 0.001 TRP E 111 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00258 (35159) covalent geometry : angle 0.59686 (47932) SS BOND : bond 0.00262 ( 48) SS BOND : angle 1.20453 ( 96) hydrogen bonds : bond 0.04526 ( 1208) hydrogen bonds : angle 5.51374 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 192 time to evaluate : 1.346 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: A 549 GLU cc_start: 0.3411 (OUTLIER) cc_final: 0.3112 (tp30) REVERT: A 795 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 833 GLN cc_start: 0.8432 (mt0) cc_final: 0.8034 (mt0) REVERT: A 1012 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7185 (t80) REVERT: B 161 MET cc_start: 0.6329 (tmm) cc_final: 0.5949 (tmm) REVERT: B 183 PHE cc_start: 0.5395 (p90) cc_final: 0.4287 (p90) REVERT: B 240 MET cc_start: 0.4134 (mpp) cc_final: 0.3880 (mpp) REVERT: B 620 CYS cc_start: 0.3213 (OUTLIER) cc_final: 0.2802 (m) REVERT: B 662 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.5691 (tp) REVERT: B 970 ILE cc_start: 0.4886 (mm) cc_final: 0.4578 (tt) REVERT: C 1137 MET cc_start: 0.7586 (mpp) cc_final: 0.7363 (mpp) REVERT: E 34 MET cc_start: 0.2902 (mpp) cc_final: 0.1954 (tmm) REVERT: G 83 MET cc_start: 0.5219 (mtm) cc_final: 0.5016 (mpp) outliers start: 109 outliers final: 86 residues processed: 287 average time/residue: 0.1908 time to fit residues: 94.2106 Evaluate side-chains 269 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 178 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 226 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 391 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 301 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 171 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.103425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.089855 restraints weight = 465472.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.088730 restraints weight = 674867.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.089290 restraints weight = 450745.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.090444 restraints weight = 298570.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.090243 restraints weight = 243171.478| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35207 Z= 0.166 Angle : 0.653 9.569 48028 Z= 0.345 Chirality : 0.044 0.210 5550 Planarity : 0.005 0.058 6205 Dihedral : 5.831 56.059 5016 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.86 % Favored : 93.85 % Rotamer: Outliers : 3.75 % Allowed : 16.92 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4595 helix: 1.29 (0.19), residues: 771 sheet: 0.59 (0.15), residues: 1190 loop : -1.40 (0.11), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1179 TYR 0.027 0.002 TYR C 641 PHE 0.022 0.002 PHE C1136 TRP 0.019 0.002 TRP A 553 HIS 0.006 0.001 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.00359 (35159) covalent geometry : angle 0.65057 (47932) SS BOND : bond 0.00377 ( 48) SS BOND : angle 1.41106 ( 96) hydrogen bonds : bond 0.04772 ( 1208) hydrogen bonds : angle 5.67938 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 200 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 GLU cc_start: 0.3819 (OUTLIER) cc_final: 0.3346 (tp30) REVERT: A 795 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7819 (mm) REVERT: A 833 GLN cc_start: 0.8550 (mt0) cc_final: 0.8077 (mt0) REVERT: A 1012 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.6981 (t80) REVERT: B 183 PHE cc_start: 0.4207 (p90) cc_final: 0.3518 (p90) REVERT: B 240 MET cc_start: 0.4811 (mpp) cc_final: 0.4446 (mpp) REVERT: B 477 THR cc_start: -0.1334 (OUTLIER) cc_final: -0.1574 (p) REVERT: B 563 MET cc_start: 0.3311 (mmm) cc_final: 0.3055 (mmm) REVERT: B 620 CYS cc_start: 0.3187 (OUTLIER) cc_final: 0.2833 (m) REVERT: B 662 ILE cc_start: 0.6025 (OUTLIER) cc_final: 0.5585 (tp) REVERT: B 757 MET cc_start: 0.2812 (tpp) cc_final: 0.2567 (mmm) REVERT: B 970 ILE cc_start: 0.5108 (mm) cc_final: 0.4563 (tt) REVERT: C 171 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7260 (pt) REVERT: E 6 GLU cc_start: 0.4501 (OUTLIER) cc_final: 0.3081 (tp30) REVERT: E 32 TYR cc_start: 0.5422 (OUTLIER) cc_final: 0.4545 (m-80) REVERT: F 7 MET cc_start: 0.3996 (tmm) cc_final: 0.3574 (tmm) REVERT: G 83 MET cc_start: 0.5076 (mtm) cc_final: 0.4549 (mpp) REVERT: I 32 TYR cc_start: 0.6732 (m-80) cc_final: 0.6466 (m-80) outliers start: 137 outliers final: 104 residues processed: 316 average time/residue: 0.1848 time to fit residues: 100.2863 Evaluate side-chains 291 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 178 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 374 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 365 optimal weight: 0.7980 chunk 256 optimal weight: 0.0370 chunk 320 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 260 optimal weight: 10.0000 chunk 340 optimal weight: 0.4980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 171 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.104455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.078455 restraints weight = 309167.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.073831 restraints weight = 367769.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.073229 restraints weight = 421734.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.072876 restraints weight = 370421.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.072961 restraints weight = 286128.644| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35207 Z= 0.112 Angle : 0.594 10.263 48028 Z= 0.310 Chirality : 0.042 0.189 5550 Planarity : 0.004 0.045 6205 Dihedral : 5.409 58.586 5014 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.90 % Favored : 94.84 % Rotamer: Outliers : 2.68 % Allowed : 18.13 % Favored : 79.19 % 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: -0.41 (0.12), residues: 4595 helix: 1.70 (0.19), residues: 766 sheet: 0.62 (0.15), residues: 1201 loop : -1.38 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 401 TYR 0.025 0.001 TYR C 641 PHE 0.021 0.001 PHE A 281 TRP 0.030 0.001 TRP E 111 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00236 (35159) covalent geometry : angle 0.59279 (47932) SS BOND : bond 0.00228 ( 48) SS BOND : angle 1.12772 ( 96) hydrogen bonds : bond 0.04326 ( 1208) hydrogen bonds : angle 5.41072 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 196 time to evaluate : 1.417 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: A 549 GLU cc_start: 0.3567 (OUTLIER) cc_final: 0.3212 (tp30) REVERT: A 795 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7820 (mm) REVERT: A 833 GLN cc_start: 0.8319 (mt0) cc_final: 0.8066 (mt0) REVERT: A 1012 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7531 (t80) REVERT: B 161 MET cc_start: 0.5935 (tmm) cc_final: 0.5729 (tmm) REVERT: B 183 PHE cc_start: 0.4738 (p90) cc_final: 0.4013 (p90) REVERT: B 240 MET cc_start: 0.4690 (mpp) cc_final: 0.4484 (mpp) REVERT: B 477 THR cc_start: -0.1521 (OUTLIER) cc_final: -0.1812 (p) REVERT: B 620 CYS cc_start: 0.2920 (OUTLIER) cc_final: 0.2592 (m) REVERT: B 662 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.5451 (tp) REVERT: B 970 ILE cc_start: 0.4730 (mm) cc_final: 0.4414 (tt) REVERT: C 171 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7385 (pt) REVERT: C 641 TYR cc_start: 0.3775 (OUTLIER) cc_final: 0.0782 (p90) REVERT: D 186 LEU cc_start: 0.2382 (OUTLIER) cc_final: 0.2041 (tp) REVERT: E 6 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4686 (tp30) REVERT: G 83 MET cc_start: 0.5195 (mtm) cc_final: 0.4980 (mpp) REVERT: I 32 TYR cc_start: 0.7525 (m-80) cc_final: 0.7220 (m-80) outliers start: 98 outliers final: 71 residues processed: 286 average time/residue: 0.1876 time to fit residues: 91.9185 Evaluate side-chains 259 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 353 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 366 optimal weight: 30.0000 chunk 186 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 228 optimal weight: 0.3980 chunk 101 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 264 HIS A 766 HIS A 848 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 GLN D 6 GLN D 171 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN H 165 GLN I 35 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.101702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.088015 restraints weight = 419935.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.086914 restraints weight = 564416.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.087336 restraints weight = 393997.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.088004 restraints weight = 263345.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.087749 restraints weight = 262296.804| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 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 = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 35207 Z= 0.237 Angle : 0.764 11.282 48028 Z= 0.408 Chirality : 0.047 0.281 5550 Planarity : 0.005 0.064 6205 Dihedral : 6.465 56.952 5014 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.70 % Rotamer: Outliers : 3.15 % Allowed : 18.04 % Favored : 78.81 % 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: -1.05 (0.12), residues: 4595 helix: 0.67 (0.18), residues: 767 sheet: 0.20 (0.15), residues: 1198 loop : -1.62 (0.11), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 979 TYR 0.042 0.003 TYR B 274 PHE 0.030 0.003 PHE C 204 TRP 0.025 0.003 TRP B 253 HIS 0.010 0.002 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00513 (35159) covalent geometry : angle 0.76145 (47932) SS BOND : bond 0.00524 ( 48) SS BOND : angle 1.55404 ( 96) hydrogen bonds : bond 0.05349 ( 1208) hydrogen bonds : angle 6.12278 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 193 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8166 (mmp) cc_final: 0.7827 (mmt) REVERT: A 549 GLU cc_start: 0.4160 (OUTLIER) cc_final: 0.3463 (tp30) REVERT: A 795 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7941 (mm) REVERT: B 183 PHE cc_start: 0.4323 (p90) cc_final: 0.3568 (p90) REVERT: B 620 CYS cc_start: 0.3359 (OUTLIER) cc_final: 0.3136 (m) REVERT: B 662 ILE cc_start: 0.5846 (OUTLIER) cc_final: 0.5391 (tp) REVERT: B 970 ILE cc_start: 0.5681 (mm) cc_final: 0.5465 (tt) REVERT: C 641 TYR cc_start: 0.3789 (OUTLIER) cc_final: 0.0738 (p90) REVERT: D 7 MET cc_start: 0.5116 (tmm) cc_final: 0.4375 (tmm) REVERT: E 6 GLU cc_start: 0.4120 (OUTLIER) cc_final: 0.2770 (tp30) REVERT: I 32 TYR cc_start: 0.6731 (m-80) cc_final: 0.6498 (m-80) outliers start: 115 outliers final: 85 residues processed: 297 average time/residue: 0.1859 time to fit residues: 95.5712 Evaluate side-chains 263 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 172 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 258 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 415 optimal weight: 30.0000 chunk 248 optimal weight: 10.0000 chunk 438 optimal weight: 8.9990 chunk 305 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 428 optimal weight: 0.9980 chunk 451 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 GLN D 171 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** 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 = 0.4339 r_free = 0.4339 target = 0.101813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.085908 restraints weight = 402424.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.084506 restraints weight = 484225.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.084339 restraints weight = 418385.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.084475 restraints weight = 319735.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.084735 restraints weight = 285375.895| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 35207 Z= 0.236 Angle : 0.857 59.198 48028 Z= 0.465 Chirality : 0.046 0.248 5550 Planarity : 0.005 0.060 6205 Dihedral : 6.434 56.964 5012 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.04 % Favored : 92.74 % Rotamer: Outliers : 2.74 % Allowed : 18.65 % Favored : 78.61 % Cbeta Deviations : 0.05 % 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: -1.10 (0.12), residues: 4595 helix: 0.63 (0.18), residues: 767 sheet: 0.19 (0.15), residues: 1192 loop : -1.66 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 401 TYR 0.067 0.003 TYR C 270 PHE 0.100 0.003 PHE B 418 TRP 0.022 0.002 TRP B 253 HIS 0.009 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00524 (35159) covalent geometry : angle 0.85473 (47932) SS BOND : bond 0.00637 ( 48) SS BOND : angle 1.64673 ( 96) hydrogen bonds : bond 0.05269 ( 1208) hydrogen bonds : angle 6.10529 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9190 Ramachandran restraints generated. 4595 Oldfield, 0 Emsley, 4595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 172 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.8401 (mmp) cc_final: 0.8154 (mmt) REVERT: A 549 GLU cc_start: 0.4026 (OUTLIER) cc_final: 0.3374 (tp30) REVERT: A 795 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7838 (mm) REVERT: B 183 PHE cc_start: 0.4513 (p90) cc_final: 0.3780 (p90) REVERT: B 620 CYS cc_start: 0.3374 (OUTLIER) cc_final: 0.3147 (m) REVERT: B 662 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5352 (tp) REVERT: B 970 ILE cc_start: 0.5645 (mm) cc_final: 0.5402 (tt) REVERT: C 641 TYR cc_start: 0.3919 (OUTLIER) cc_final: 0.0836 (p90) REVERT: D 6 GLN cc_start: 0.5357 (OUTLIER) cc_final: 0.5118 (pm20) REVERT: D 7 MET cc_start: 0.5580 (tmm) cc_final: 0.5110 (tmm) REVERT: E 6 GLU cc_start: 0.4721 (OUTLIER) cc_final: 0.3458 (tp30) REVERT: I 32 TYR cc_start: 0.7082 (m-80) cc_final: 0.6745 (m-80) outliers start: 100 outliers final: 89 residues processed: 263 average time/residue: 0.1908 time to fit residues: 85.5588 Evaluate side-chains 266 residues out of total 4021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 170 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 641 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 577 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 620 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 0 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 439 optimal weight: 0.0970 chunk 356 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 358 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 300 optimal weight: 0.5980 chunk 397 optimal weight: 9.9990 overall best weight: 4.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.101804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.085638 restraints weight = 367041.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.082752 restraints weight = 391036.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.082611 restraints weight = 475676.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.082953 restraints weight = 339951.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.083160 restraints weight = 271798.908| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 35207 Z= 0.236 Angle : 0.857 59.198 48028 Z= 0.465 Chirality : 0.046 0.248 5550 Planarity : 0.005 0.060 6205 Dihedral : 6.434 56.964 5012 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.04 % Favored : 92.74 % Rotamer: Outliers : 2.63 % Allowed : 18.81 % Favored : 78.56 % Cbeta Deviations : 0.05 % 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: -1.10 (0.12), residues: 4595 helix: 0.63 (0.18), residues: 767 sheet: 0.19 (0.15), residues: 1192 loop : -1.66 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 401 TYR 0.067 0.003 TYR C 270 PHE 0.100 0.003 PHE B 418 TRP 0.022 0.002 TRP B 253 HIS 0.009 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00524 (35159) covalent geometry : angle 0.85474 (47932) SS BOND : bond 0.00637 ( 48) SS BOND : angle 1.64673 ( 96) hydrogen bonds : bond 0.05269 ( 1208) hydrogen bonds : angle 6.10529 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9881.97 seconds wall clock time: 169 minutes 31.13 seconds (10171.13 seconds total)