Starting phenix.real_space_refine on Wed Mar 20 23:59:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz1_32218/03_2024/7vz1_32218_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 188 5.16 5 C 17732 2.51 5 N 4886 2.21 5 O 5890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M GLU 217": "OE1" <-> "OE2" Residue "M GLU 269": "OE1" <-> "OE2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M GLU 628": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 85": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O ARG 42": "NH1" <-> "NH2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q ARG 107": "NH1" <-> "NH2" Residue "Q GLU 156": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 335": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28737 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1408 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2351 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3044 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 20, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 5, 'TRANS': 23} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "M" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 188 Classifications: {'water': 188} Link IDs: {None: 187} Chain: "N" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "Q" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 47.173 49.580 102.898 1.00 9.11 S ATOM 3048 SG CYS A 425 46.719 45.900 108.411 1.00 17.70 S ATOM 2726 SG CYS A 385 44.018 45.147 102.621 1.00 4.48 S ATOM 2687 SG CYS A 379 42.032 49.832 107.036 1.00 8.97 S ATOM 3945 SG CYS B 113 34.334 67.403 69.404 1.00 1.16 S ATOM 3964 SG CYS B 116 39.630 64.923 72.860 1.00 8.33 S ATOM 3987 SG CYS B 119 40.403 68.074 67.474 1.00 7.32 S ATOM 4316 SG CYS B 162 37.878 62.187 67.873 1.00 3.29 S ATOM 4014 SG CYS B 123 46.201 71.174 62.828 1.00 0.00 S ATOM 4240 SG CYS B 152 44.169 69.887 56.890 1.00 3.13 S ATOM 4287 SG CYS B 158 42.534 65.811 61.763 1.00 10.01 S ATOM 4266 SG CYS B 155 48.426 66.084 59.865 1.00 0.00 S ATOM 5708 SG CYS C 166 50.420 70.351 52.516 1.00 4.04 S ATOM 4980 SG CYS C 72 50.933 72.111 46.191 1.00 3.36 S ATOM 4974 SG CYS C 71 55.957 70.182 48.534 1.00 0.00 S ATOM 5478 SG CYS C 136 52.815 75.067 51.084 1.00 1.91 S ATOM 14526 SG CYS M 131 39.314 64.113 85.005 1.00 5.86 S ATOM 14505 SG CYS M 128 42.926 60.118 81.345 1.00 9.06 S ATOM 14566 SG CYS M 137 45.250 63.132 86.761 1.00 12.83 S ATOM 14898 SG CYS M 179 43.956 62.498 98.074 1.00 9.35 S ATOM 15252 SG CYS M 226 40.571 65.424 94.012 1.00 6.08 S ATOM 14922 SG CYS M 182 38.550 64.954 100.144 1.00 10.52 S ATOM 14875 SG CYS M 176 38.158 59.762 96.350 1.00 10.08 S ATOM 14123 SG CYS M 78 55.648 57.538 100.919 1.00 10.35 S ATOM 14224 SG CYS M 92 53.986 59.609 103.414 1.00 11.78 S ATOM 14012 SG CYS M 64 49.501 59.534 101.465 1.00 1.40 S ATOM 14098 SG CYS M 75 50.426 57.948 98.233 1.00 7.85 S ATOM 21061 SG CYS O 135 31.399 31.481 110.397 1.00 30.57 S ATOM 21095 SG CYS O 140 31.400 27.938 111.316 1.00 35.42 S ATOM 21375 SG CYS O 176 35.970 32.749 112.857 1.00 25.86 S ATOM 21398 SG CYS O 180 36.551 29.559 113.725 1.00 32.49 S ATOM 27156 SG CYS T 86 27.347 53.707 76.743 1.00 19.19 S ATOM 27334 SG CYS T 111 28.596 57.106 77.822 1.00 15.80 S Time building chain proxies: 15.91, per 1000 atoms: 0.55 Number of scatterers: 28737 At special positions: 0 Unit cell: (121.867, 143.276, 158.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 188 16.00 P 11 15.00 Mg 1 11.99 O 5890 8.00 N 4886 7.00 C 17732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.83 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 24 sheets defined 38.9% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.87 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.621A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.949A pdb=" N THR A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.393A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.534A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 6.031A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 123 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.287A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.278A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.754A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.007A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.072A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.803A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 220 removed outlier: 3.959A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 323 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 349 through 356 removed outlier: 5.352A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.619A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.372A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.502A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.710A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.186A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.520A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 396 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 480 No H-bonds generated for 'chain 'M' and resid 478 through 480' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 665 through 673 removed outlier: 3.751A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.643A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.446A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.845A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.950A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.804A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.033A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.224A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.706A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 4.511A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.196A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 73 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.108A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.024A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.397A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 7.013A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.488A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= L, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= M, first strand: chain 'M' and resid 246 through 251 removed outlier: 3.591A pdb=" N ARG M 272 " --> pdb=" O SER M 264 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= O, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.575A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.170A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= R, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.394A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.709A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.733A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= V, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.532A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= X, first strand: chain 'T' and resid 83 through 86 912 hydrogen bonds defined for protein. 2472 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: 9.61 Time building geometry restraints manager: 13.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 11550 1.40 - 1.63: 16761 1.63 - 1.85: 279 1.85 - 2.08: 0 2.08 - 2.31: 80 Bond restraints: 28670 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.288 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C2B NDP J 401 " pdb=" C3B NDP J 401 " ideal model delta sigma weight residual 1.552 1.236 0.316 3.50e-02 8.16e+02 8.16e+01 ... (remaining 28665 not shown) Histogram of bond angle deviations from ideal: 73.35 - 85.80: 76 85.80 - 98.24: 0 98.24 - 110.69: 8741 110.69 - 123.13: 28494 123.13 - 135.57: 1528 Bond angle restraints: 38839 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 125.37 -17.63 1.95e+00 2.62e-01 8.14e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.12 -14.28 1.91e+00 2.73e-01 5.56e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.50 7.96 1.17e+00 7.36e-01 4.66e+01 angle pdb=" C ARG A 405 " pdb=" N PRO A 406 " pdb=" CA PRO A 406 " ideal model delta sigma weight residual 119.05 126.55 -7.50 1.11e+00 8.12e-01 4.56e+01 angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 120.16 -8.83 1.32e+00 5.72e-01 4.46e+01 ... (remaining 38834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 16687 34.92 - 69.83: 634 69.83 - 104.75: 59 104.75 - 139.66: 4 139.66 - 174.58: 2 Dihedral angle restraints: 17386 sinusoidal: 7323 harmonic: 10063 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 72.17 -174.58 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -135.06 49.06 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 17383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3759 0.075 - 0.150: 444 0.150 - 0.224: 12 0.224 - 0.299: 3 0.299 - 0.374: 2 Chirality restraints: 4220 Sorted by residual: chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA LYS J 370 " pdb=" N LYS J 370 " pdb=" C LYS J 370 " pdb=" CB LYS J 370 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.43 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 4217 not shown) Planarity restraints: 4996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.102 2.00e-02 2.50e+03 2.39e-01 7.12e+02 pdb=" C3N NDP J 401 " 0.407 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.060 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.267 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.111 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C2N NDP J 401 " 0.116 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.117 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP J 401 " -0.053 2.00e-02 2.50e+03 7.61e-02 5.78e+01 pdb=" C5N NDP J 401 " 0.093 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " -0.094 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " 0.053 2.00e-02 2.50e+03 ... (remaining 4993 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2757 2.74 - 3.28: 28360 3.28 - 3.82: 52071 3.82 - 4.36: 66251 4.36 - 4.90: 104477 Nonbonded interactions: 253916 Sorted by model distance: nonbonded pdb=" O HOH C 412 " pdb=" O HOH C 454 " model vdw 2.201 2.440 nonbonded pdb=" OD1 ASP M 162 " pdb=" O HOH M 901 " model vdw 2.206 2.440 nonbonded pdb=" O HOH Q 509 " pdb=" O HOH Q 654 " model vdw 2.208 2.440 nonbonded pdb=" ND2 ASN L 109 " pdb=" O LEU L 111 " model vdw 2.214 2.520 nonbonded pdb=" O PRO Q 366 " pdb=" O HOH Q 501 " model vdw 2.219 2.440 ... (remaining 253911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.430 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: 23.910 Check model and map are aligned: 0.510 Set scattering table: 0.270 Process input model: 89.560 Find NCS groups from input model: 0.830 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 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 : 0.008 0.316 28670 Z= 0.527 Angle : 0.779 17.629 38839 Z= 0.414 Chirality : 0.047 0.374 4220 Planarity : 0.007 0.239 4996 Dihedral : 17.447 174.579 10911 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 1.17 % Allowed : 15.98 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3439 helix: 0.71 (0.14), residues: 1343 sheet: 0.30 (0.26), residues: 382 loop : -0.42 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 104 HIS 0.013 0.001 HIS Q 223 PHE 0.016 0.002 PHE M 238 TYR 0.019 0.002 TYR P 64 ARG 0.007 0.001 ARG Q 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 432 time to evaluate : 3.199 Fit side-chains REVERT: A 29 LYS cc_start: 0.6162 (ttmt) cc_final: 0.5584 (mptm) REVERT: F 35 ASP cc_start: 0.7660 (m-30) cc_final: 0.7417 (m-30) REVERT: F 57 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: H 73 GLN cc_start: 0.8050 (mm110) cc_final: 0.7439 (mt0) REVERT: K 98 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: M 217 GLU cc_start: 0.8559 (pm20) cc_final: 0.8322 (pm20) outliers start: 35 outliers final: 25 residues processed: 459 average time/residue: 1.7769 time to fit residues: 927.2491 Evaluate side-chains 443 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 416 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 365 SER Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 0.7980 chunk 256 optimal weight: 6.9990 chunk 142 optimal weight: 0.5980 chunk 87 optimal weight: 0.0020 chunk 173 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 overall best weight: 2.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 59 GLN C 123 GLN I 110 GLN J 171 ASN J 251 ASN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 39 GLN M 453 GLN M 459 ASN M 667 GLN N 52 ASN N 69 ASN N 112 ASN O 41 HIS ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 431 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.0459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28670 Z= 0.277 Angle : 0.613 10.952 38839 Z= 0.321 Chirality : 0.046 0.199 4220 Planarity : 0.005 0.068 4996 Dihedral : 10.162 173.855 4102 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 3.48 % Allowed : 14.04 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3439 helix: 0.71 (0.14), residues: 1348 sheet: 0.26 (0.26), residues: 388 loop : -0.38 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 422 HIS 0.010 0.001 HIS Q 223 PHE 0.020 0.002 PHE M 238 TYR 0.020 0.002 TYR P 64 ARG 0.008 0.001 ARG Q 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 421 time to evaluate : 3.208 Fit side-chains REVERT: A 29 LYS cc_start: 0.6205 (ttmt) cc_final: 0.5586 (mptm) REVERT: A 232 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: A 301 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: A 456 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: C 113 MET cc_start: 0.9506 (tpt) cc_final: 0.9169 (tpt) REVERT: E 37 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7680 (mtp180) REVERT: F 35 ASP cc_start: 0.7654 (m-30) cc_final: 0.7405 (m-30) REVERT: F 57 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: H 73 GLN cc_start: 0.8078 (mm110) cc_final: 0.7529 (mt0) REVERT: H 95 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8402 (tp) REVERT: L 86 ASN cc_start: 0.9439 (OUTLIER) cc_final: 0.9166 (t0) REVERT: M 643 ARG cc_start: 0.9407 (OUTLIER) cc_final: 0.7228 (mtt-85) REVERT: Q 197 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.6787 (ppp) REVERT: T 105 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6287 (mp0) outliers start: 104 outliers final: 46 residues processed: 483 average time/residue: 1.7506 time to fit residues: 962.5708 Evaluate side-chains 466 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 410 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 539 LYS Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 333 optimal weight: 0.5980 chunk 274 optimal weight: 3.9990 chunk 305 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 59 GLN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 453 GLN M 459 ASN M 499 ASN O 182 ASN Q 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28670 Z= 0.210 Angle : 0.556 10.689 38839 Z= 0.291 Chirality : 0.044 0.189 4220 Planarity : 0.005 0.066 4996 Dihedral : 9.682 175.181 4086 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 3.07 % Allowed : 14.81 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3439 helix: 0.79 (0.14), residues: 1348 sheet: 0.25 (0.26), residues: 388 loop : -0.34 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 422 HIS 0.008 0.001 HIS Q 223 PHE 0.015 0.001 PHE M 238 TYR 0.019 0.001 TYR P 64 ARG 0.006 0.000 ARG O 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 425 time to evaluate : 3.858 Fit side-chains REVERT: A 29 LYS cc_start: 0.6238 (ttmt) cc_final: 0.5584 (mptm) REVERT: A 232 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: A 301 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: A 456 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: C 113 MET cc_start: 0.9501 (tpt) cc_final: 0.9172 (tpt) REVERT: E 37 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7688 (mtp180) REVERT: F 35 ASP cc_start: 0.7595 (m-30) cc_final: 0.7366 (m-30) REVERT: F 57 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: H 73 GLN cc_start: 0.8049 (mm110) cc_final: 0.7508 (mt0) REVERT: H 95 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8366 (tp) REVERT: Q 197 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6706 (ppp) REVERT: T 105 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6318 (mp0) outliers start: 92 outliers final: 50 residues processed: 478 average time/residue: 1.7142 time to fit residues: 933.7223 Evaluate side-chains 473 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 415 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 309 optimal weight: 0.6980 chunk 327 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 59 GLN J 171 ASN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 453 GLN M 459 ASN M 499 ASN Q 270 ASN Q 454 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28670 Z= 0.198 Angle : 0.540 10.697 38839 Z= 0.281 Chirality : 0.043 0.187 4220 Planarity : 0.005 0.064 4996 Dihedral : 9.333 175.996 4086 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 3.34 % Allowed : 14.94 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3439 helix: 0.86 (0.14), residues: 1350 sheet: 0.23 (0.26), residues: 389 loop : -0.29 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.014 0.001 PHE N 55 TYR 0.018 0.001 TYR P 64 ARG 0.007 0.000 ARG Q 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 429 time to evaluate : 3.489 Fit side-chains REVERT: A 29 LYS cc_start: 0.6261 (ttmt) cc_final: 0.5589 (mptm) REVERT: A 232 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: A 301 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: A 456 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: B 114 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9286 (pp) REVERT: E 37 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7669 (mtp180) REVERT: F 35 ASP cc_start: 0.7569 (m-30) cc_final: 0.7356 (m-30) REVERT: F 57 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: H 73 GLN cc_start: 0.8025 (mm110) cc_final: 0.7506 (mt0) REVERT: H 95 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8355 (tp) REVERT: I 29 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7583 (mm110) REVERT: J 85 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8697 (ppt170) REVERT: K 102 SER cc_start: 0.9016 (t) cc_final: 0.8816 (m) REVERT: L 156 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: M 215 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6258 (tpt) REVERT: M 382 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8084 (mtt180) REVERT: M 643 ARG cc_start: 0.9392 (OUTLIER) cc_final: 0.7216 (mtt-85) REVERT: O 64 GLU cc_start: 0.7822 (tt0) cc_final: 0.7472 (tt0) REVERT: T 105 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6410 (mp0) outliers start: 100 outliers final: 51 residues processed: 488 average time/residue: 1.7696 time to fit residues: 981.3246 Evaluate side-chains 485 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 420 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.9990 chunk 186 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 59 GLN E 58 GLN E 99 GLN I 25 GLN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 453 GLN M 459 ASN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28670 Z= 0.196 Angle : 0.536 10.646 38839 Z= 0.280 Chirality : 0.043 0.187 4220 Planarity : 0.005 0.062 4996 Dihedral : 9.155 176.204 4084 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 3.24 % Allowed : 15.44 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3439 helix: 0.89 (0.14), residues: 1350 sheet: 0.20 (0.26), residues: 389 loop : -0.28 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.014 0.001 PHE N 55 TYR 0.018 0.001 TYR P 64 ARG 0.006 0.000 ARG Q 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 428 time to evaluate : 3.097 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.6305 (ttmt) cc_final: 0.5603 (mptm) REVERT: A 232 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: A 301 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 401 LYS cc_start: 0.7746 (mttt) cc_final: 0.7536 (mtmt) REVERT: A 456 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: B 114 ILE cc_start: 0.9598 (OUTLIER) cc_final: 0.9280 (pp) REVERT: C 65 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8168 (tmm) REVERT: E 37 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7656 (mtp180) REVERT: E 51 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: F 35 ASP cc_start: 0.7569 (m-30) cc_final: 0.7354 (m-30) REVERT: F 57 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: H 73 GLN cc_start: 0.8029 (mm110) cc_final: 0.7520 (mt0) REVERT: H 95 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8350 (tp) REVERT: I 29 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7578 (mm110) REVERT: J 85 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8618 (ppt170) REVERT: J 214 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8636 (mp) REVERT: K 102 SER cc_start: 0.9029 (t) cc_final: 0.8818 (m) REVERT: L 156 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8321 (mttp) REVERT: M 215 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6359 (tpt) REVERT: M 643 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.7214 (mtt-85) REVERT: O 64 GLU cc_start: 0.7832 (tt0) cc_final: 0.7528 (tt0) REVERT: O 222 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6759 (ttm170) REVERT: T 105 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6413 (mp0) outliers start: 97 outliers final: 51 residues processed: 490 average time/residue: 1.6788 time to fit residues: 937.9815 Evaluate side-chains 483 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 415 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 80 optimal weight: 0.0870 chunk 327 optimal weight: 6.9990 chunk 272 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 59 GLN E 99 GLN I 25 GLN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 74 ASN M 453 GLN M 459 ASN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28670 Z= 0.181 Angle : 0.523 10.657 38839 Z= 0.272 Chirality : 0.043 0.185 4220 Planarity : 0.004 0.061 4996 Dihedral : 8.915 176.784 4080 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 2.97 % Allowed : 15.74 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3439 helix: 0.95 (0.14), residues: 1349 sheet: 0.24 (0.26), residues: 383 loop : -0.26 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.013 0.001 PHE B 175 TYR 0.017 0.001 TYR P 64 ARG 0.006 0.000 ARG J 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 425 time to evaluate : 3.703 Fit side-chains REVERT: A 29 LYS cc_start: 0.6331 (tttt) cc_final: 0.5606 (mptm) REVERT: A 232 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: A 301 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: A 401 LYS cc_start: 0.7669 (mttt) cc_final: 0.7444 (mtmt) REVERT: A 456 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: B 114 ILE cc_start: 0.9596 (OUTLIER) cc_final: 0.9283 (pp) REVERT: E 37 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7775 (mtp180) REVERT: E 51 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: G 123 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7312 (mt-10) REVERT: H 73 GLN cc_start: 0.8015 (mm110) cc_final: 0.7526 (mt0) REVERT: I 29 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7585 (mm110) REVERT: I 70 MET cc_start: 0.8254 (tmt) cc_final: 0.7953 (tmt) REVERT: J 85 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8617 (ppt170) REVERT: J 214 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8635 (mp) REVERT: K 102 SER cc_start: 0.9029 (t) cc_final: 0.8809 (m) REVERT: L 156 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8349 (mttp) REVERT: M 215 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6304 (tpt) REVERT: M 643 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.7193 (mtt-85) REVERT: O 42 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7988 (ptp-170) REVERT: O 64 GLU cc_start: 0.7816 (tt0) cc_final: 0.7522 (tt0) REVERT: T 105 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6412 (mp0) outliers start: 89 outliers final: 49 residues processed: 479 average time/residue: 1.7534 time to fit residues: 956.8485 Evaluate side-chains 479 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 416 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 276 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 59 GLN E 58 GLN E 99 GLN F 62 GLN H 50 GLN I 25 GLN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 453 GLN M 459 ASN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 28670 Z= 0.358 Angle : 0.657 11.091 38839 Z= 0.346 Chirality : 0.049 0.219 4220 Planarity : 0.006 0.067 4996 Dihedral : 9.302 172.888 4077 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 3.48 % Allowed : 15.44 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3439 helix: 0.63 (0.14), residues: 1367 sheet: 0.19 (0.26), residues: 373 loop : -0.35 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 171 HIS 0.009 0.001 HIS J 37 PHE 0.020 0.002 PHE N 55 TYR 0.019 0.002 TYR P 64 ARG 0.010 0.001 ARG Q 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 423 time to evaluate : 3.771 Fit side-chains REVERT: A 29 LYS cc_start: 0.6446 (tttt) cc_final: 0.5692 (mptm) REVERT: A 232 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8374 (m-30) REVERT: A 301 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: A 401 LYS cc_start: 0.8045 (mttt) cc_final: 0.7684 (mtmt) REVERT: A 456 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.7039 (tt0) REVERT: B 114 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9302 (pp) REVERT: C 99 GLN cc_start: 0.8146 (pt0) cc_final: 0.7875 (mt0) REVERT: C 113 MET cc_start: 0.9506 (tpt) cc_final: 0.9220 (tpt) REVERT: E 37 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7607 (mtp180) REVERT: E 51 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: F 91 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8419 (mp) REVERT: H 73 GLN cc_start: 0.8100 (mm110) cc_final: 0.7599 (mt0) REVERT: H 95 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8423 (tp) REVERT: I 29 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7694 (mm110) REVERT: I 70 MET cc_start: 0.8446 (tmt) cc_final: 0.8215 (tmt) REVERT: J 85 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8818 (ppt170) REVERT: J 214 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8631 (mp) REVERT: K 102 SER cc_start: 0.9091 (t) cc_final: 0.8847 (m) REVERT: L 156 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: M 215 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6257 (tpt) REVERT: M 636 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.7707 (p90) REVERT: M 643 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.7437 (mtt-85) REVERT: M 696 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7217 (mtt) REVERT: O 64 GLU cc_start: 0.7974 (tt0) cc_final: 0.7683 (tt0) REVERT: O 222 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6799 (ttm170) REVERT: T 105 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6500 (mp0) outliers start: 104 outliers final: 53 residues processed: 483 average time/residue: 1.8570 time to fit residues: 1035.3601 Evaluate side-chains 488 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 417 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 252 SER Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain W residue 22 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 30 optimal weight: 0.0030 chunk 256 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN E 58 GLN E 99 GLN I 25 GLN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 453 GLN M 459 ASN M 499 ASN Q 270 ASN T 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 28670 Z= 0.146 Angle : 0.503 10.981 38839 Z= 0.262 Chirality : 0.042 0.175 4220 Planarity : 0.004 0.063 4996 Dihedral : 8.664 178.116 4077 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.07 % Allowed : 17.15 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3439 helix: 0.93 (0.14), residues: 1350 sheet: 0.22 (0.26), residues: 383 loop : -0.29 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.014 0.001 PHE B 175 TYR 0.017 0.001 TYR P 64 ARG 0.007 0.000 ARG J 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 426 time to evaluate : 3.568 Fit side-chains REVERT: A 29 LYS cc_start: 0.6376 (tttt) cc_final: 0.5629 (mptm) REVERT: A 232 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: A 301 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: A 401 LYS cc_start: 0.7552 (mttt) cc_final: 0.7321 (mtmt) REVERT: B 114 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9257 (pp) REVERT: C 99 GLN cc_start: 0.8126 (pt0) cc_final: 0.7856 (mt0) REVERT: E 37 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7702 (mtp180) REVERT: E 51 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: G 87 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7472 (mm) REVERT: G 123 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7105 (mt-10) REVERT: H 73 GLN cc_start: 0.8012 (mm110) cc_final: 0.7557 (mt0) REVERT: I 10 LEU cc_start: 0.8172 (mt) cc_final: 0.7923 (mt) REVERT: I 30 GLU cc_start: 0.8813 (pm20) cc_final: 0.8493 (pm20) REVERT: J 85 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8551 (ppt170) REVERT: K 102 SER cc_start: 0.9046 (t) cc_final: 0.8813 (m) REVERT: M 215 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6207 (tpt) REVERT: M 538 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8055 (mtt-85) REVERT: N 8 ARG cc_start: 0.7510 (mmt90) cc_final: 0.7134 (mtt-85) REVERT: O 42 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7951 (ptp-170) REVERT: O 64 GLU cc_start: 0.7806 (tt0) cc_final: 0.7521 (tt0) REVERT: T 105 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6480 (mp0) outliers start: 62 outliers final: 36 residues processed: 468 average time/residue: 1.7333 time to fit residues: 923.4136 Evaluate side-chains 457 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 410 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 538 ARG Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 285 optimal weight: 0.0770 chunk 304 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 275 optimal weight: 0.0060 chunk 287 optimal weight: 2.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN I 25 GLN I 110 GLN J 171 ASN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 453 GLN M 459 ASN M 499 ASN M 676 ASN M 678 GLN Q 270 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28670 Z= 0.191 Angle : 0.539 12.540 38839 Z= 0.280 Chirality : 0.043 0.186 4220 Planarity : 0.005 0.063 4996 Dihedral : 8.637 176.881 4077 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 2.21 % Allowed : 17.28 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3439 helix: 0.94 (0.14), residues: 1356 sheet: 0.23 (0.26), residues: 383 loop : -0.26 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.014 0.001 PHE N 55 TYR 0.018 0.001 TYR P 64 ARG 0.007 0.000 ARG J 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 415 time to evaluate : 3.763 Fit side-chains REVERT: A 29 LYS cc_start: 0.6427 (tttt) cc_final: 0.5660 (mptm) REVERT: A 232 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8344 (m-30) REVERT: A 301 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: A 401 LYS cc_start: 0.7652 (mttt) cc_final: 0.7414 (mtmt) REVERT: B 114 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9281 (pp) REVERT: C 99 GLN cc_start: 0.8128 (pt0) cc_final: 0.7864 (mt0) REVERT: E 37 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7719 (mtp180) REVERT: E 51 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: G 123 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7259 (mt-10) REVERT: H 73 GLN cc_start: 0.8023 (mm110) cc_final: 0.7568 (mt0) REVERT: H 95 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8373 (tp) REVERT: I 30 GLU cc_start: 0.8864 (pm20) cc_final: 0.8537 (pm20) REVERT: J 85 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8661 (ppt170) REVERT: K 102 SER cc_start: 0.9065 (t) cc_final: 0.8823 (m) REVERT: L 86 ASN cc_start: 0.9385 (OUTLIER) cc_final: 0.9064 (t0) REVERT: M 215 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6258 (tpt) REVERT: M 382 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8054 (mtt180) REVERT: M 538 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8090 (mtt-85) REVERT: M 643 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.7165 (mtt-85) REVERT: O 42 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8004 (ptp-170) REVERT: O 64 GLU cc_start: 0.7835 (tt0) cc_final: 0.7573 (tt0) REVERT: Q 108 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8303 (tmtt) REVERT: T 105 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6462 (mp0) outliers start: 66 outliers final: 36 residues processed: 459 average time/residue: 1.7771 time to fit residues: 925.9604 Evaluate side-chains 458 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 408 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 538 ARG Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 321 optimal weight: 0.0770 chunk 196 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 310 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 59 GLN I 25 GLN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 453 GLN M 459 ASN M 499 ASN Q 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28670 Z= 0.202 Angle : 0.545 12.882 38839 Z= 0.283 Chirality : 0.043 0.175 4220 Planarity : 0.005 0.062 4996 Dihedral : 8.637 176.606 4077 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 1.94 % Allowed : 17.31 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3439 helix: 0.94 (0.14), residues: 1349 sheet: 0.21 (0.26), residues: 383 loop : -0.27 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.014 0.001 PHE Q 382 TYR 0.018 0.001 TYR P 64 ARG 0.007 0.000 ARG J 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 411 time to evaluate : 3.534 Fit side-chains REVERT: A 29 LYS cc_start: 0.6440 (tttt) cc_final: 0.5665 (mptm) REVERT: A 232 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: A 301 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: A 401 LYS cc_start: 0.7670 (mttt) cc_final: 0.7428 (mtmt) REVERT: B 114 ILE cc_start: 0.9596 (OUTLIER) cc_final: 0.9284 (pp) REVERT: C 99 GLN cc_start: 0.8130 (pt0) cc_final: 0.7859 (mt0) REVERT: E 37 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7721 (mtp180) REVERT: E 51 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: G 123 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7246 (mt-10) REVERT: H 73 GLN cc_start: 0.8023 (mm110) cc_final: 0.7568 (mt0) REVERT: H 95 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8365 (tp) REVERT: J 85 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8676 (ppt170) REVERT: K 102 SER cc_start: 0.9062 (t) cc_final: 0.8819 (m) REVERT: L 86 ASN cc_start: 0.9386 (OUTLIER) cc_final: 0.9065 (t0) REVERT: L 156 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8318 (mttp) REVERT: M 215 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6260 (tpt) REVERT: M 382 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8060 (mtt180) REVERT: M 538 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8079 (mtt-85) REVERT: M 643 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.7165 (mtt-85) REVERT: O 42 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7969 (ptp-170) REVERT: O 64 GLU cc_start: 0.7846 (tt0) cc_final: 0.7582 (tt0) REVERT: Q 108 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8290 (tmtt) REVERT: T 105 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6479 (mp0) outliers start: 58 outliers final: 35 residues processed: 448 average time/residue: 1.7455 time to fit residues: 887.0312 Evaluate side-chains 460 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 410 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 156 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 382 ARG Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 538 ARG Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 643 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 269 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 59 GLN I 25 GLN ** J 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 453 GLN M 459 ASN M 499 ASN M 540 ASN Q 270 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.095718 restraints weight = 28655.831| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.08 r_work: 0.2769 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28670 Z= 0.242 Angle : 0.576 12.900 38839 Z= 0.301 Chirality : 0.045 0.191 4220 Planarity : 0.005 0.063 4996 Dihedral : 8.748 175.231 4077 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.11 % Allowed : 17.11 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3439 helix: 0.88 (0.14), residues: 1349 sheet: 0.16 (0.26), residues: 387 loop : -0.29 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 PHE 0.016 0.002 PHE N 55 TYR 0.018 0.002 TYR P 64 ARG 0.007 0.000 ARG J 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13571.58 seconds wall clock time: 239 minutes 52.37 seconds (14392.37 seconds total)