Starting phenix.real_space_refine (version: dev) on Mon Feb 27 06:13:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbz_31886/02_2023/7vbz_31886_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J ARG 212": "NH1" <-> "NH2" Residue "J TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 244": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "N TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ARG 142": "NH1" <-> "NH2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "Q ARG 221": "NH1" <-> "NH2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "T GLU 36": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29292 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} 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: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} 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: "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: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} 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: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} 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: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 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: "N" 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: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'970': 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "M" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 186 Classifications: {'water': 186} Link IDs: {None: 185} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} 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: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Q" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} 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 2718 SG CYS A 382 47.830 47.688 108.649 1.00 12.05 S ATOM 3060 SG CYS A 425 46.892 44.703 114.897 1.00 17.80 S ATOM 2738 SG CYS A 385 44.700 43.539 108.827 1.00 12.76 S ATOM 2699 SG CYS A 379 42.663 48.669 112.333 1.00 15.41 S ATOM 3961 SG CYS B 113 37.607 60.417 72.352 1.00 24.67 S ATOM 3980 SG CYS B 116 42.806 58.468 76.409 1.00 24.67 S ATOM 4003 SG CYS B 119 43.717 60.896 70.787 1.00 24.67 S ATOM 4332 SG CYS B 162 41.190 55.014 71.794 1.00 16.11 S ATOM 4030 SG CYS B 123 50.122 63.249 66.134 1.00 17.54 S ATOM 4256 SG CYS B 152 48.292 60.983 60.291 1.00 24.67 S ATOM 4303 SG CYS B 158 46.462 57.740 65.689 1.00 24.67 S ATOM 4282 SG CYS B 155 52.239 57.714 64.187 1.00 24.67 S ATOM 5724 SG CYS C 166 55.193 60.583 56.271 1.00 24.67 S ATOM 4996 SG CYS C 72 55.677 61.620 49.912 1.00 14.05 S ATOM 4990 SG CYS C 71 60.975 60.060 53.300 1.00 24.67 S ATOM 5494 SG CYS C 136 57.631 65.633 54.689 1.00 12.00 S ATOM 14949 SG CYS M 131 41.561 59.622 88.364 1.00 9.07 S ATOM 14928 SG CYS M 128 45.222 54.851 85.645 1.00 10.88 S ATOM 14989 SG CYS M 137 47.361 58.554 90.626 1.00 8.93 S ATOM 15321 SG CYS M 179 44.756 60.089 101.770 1.00 12.59 S ATOM 15675 SG CYS M 226 42.213 62.181 97.027 1.00 10.25 S ATOM 15345 SG CYS M 182 39.849 62.309 102.958 1.00 11.98 S ATOM 15298 SG CYS M 176 39.749 57.199 100.081 1.00 8.78 S ATOM 14546 SG CYS M 78 56.668 55.526 106.090 1.00 12.36 S ATOM 14647 SG CYS M 92 54.797 57.964 108.069 1.00 12.36 S ATOM 14435 SG CYS M 64 50.459 57.489 105.862 1.00 10.46 S ATOM 14521 SG CYS M 75 51.527 55.615 103.164 1.00 9.84 S ATOM 21484 SG CYS O 135 31.762 31.007 117.586 1.00 35.57 S ATOM 21518 SG CYS O 140 30.995 27.793 118.848 1.00 37.91 S ATOM 21798 SG CYS O 176 36.286 32.981 120.165 1.00 34.30 S ATOM 21821 SG CYS O 180 36.464 29.651 121.498 1.00 44.39 S ATOM 27631 SG CYS T 86 29.997 47.962 80.977 1.00 14.18 S ATOM 27809 SG CYS T 111 31.148 51.558 81.659 1.00 14.97 S Time building chain proxies: 16.92, per 1000 atoms: 0.58 Number of scatterers: 29292 At special positions: 0 Unit cell: (126.219, 138.572, 164.89, 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 189 16.00 P 11 15.00 Mg 1 11.99 O 5992 8.00 N 4963 7.00 C 18107 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=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.80 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " 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="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " 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="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " 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="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " 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 " 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 155 helices and 25 sheets defined 39.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 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 59 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.670A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 204 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 removed outlier: 3.896A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) 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 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' 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 removed outlier: 4.387A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.099A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.651A 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 206 removed outlier: 5.631A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.859A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) 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 122 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: 4.154A 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: 4.229A 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 39 removed outlier: 5.197A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 104 through 107 No H-bonds generated for 'chain 'G' and resid 104 through 107' Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.953A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 21 through 23 No H-bonds generated for 'chain 'I' and resid 21 through 23' 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 75 removed outlier: 4.110A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.906A 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 120 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 212 through 222 removed outlier: 3.866A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA J 218 " --> pdb=" O LEU J 214 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.905A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 335 through 337 No H-bonds generated for 'chain 'J' and resid 335 through 337' Processing helix chain 'J' and resid 345 through 348 No H-bonds generated for 'chain 'J' and resid 345 through 348' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.804A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.354A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.892A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 55 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: 3.909A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 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 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 393 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 removed outlier: 3.624A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 482 Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 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 651 through 654 Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 695 removed outlier: 4.104A pdb=" N TYR M 695 " --> pdb=" O ILE M 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 691 through 695' 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: 3.517A 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 removed outlier: 3.831A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.238A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.792A pdb=" N ASN O 90 " --> pdb=" O GLN O 87 " (cutoff:3.500A) 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 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.689A 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: 3.542A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 3.810A 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 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 120 through 126 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.734A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.558A pdb=" N TRP Q 202 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.223A 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: 4.634A 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: 4.462A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 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: 7.045A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.411A 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: 5.948A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.462A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.183A 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: 3.778A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.476A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.629A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.216A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.500A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.717A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 7.003A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.455A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 918 hydrogen bonds defined for protein. 2514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.62 Time building geometry restraints manager: 14.10 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: 11794 1.40 - 1.62: 17093 1.62 - 1.84: 273 1.84 - 2.06: 2 2.06 - 2.28: 80 Bond restraints: 29242 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 1.634 -0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C17 970 Q 501 " pdb=" O16 970 Q 501 " ideal model delta sigma weight residual 1.355 1.580 -0.225 2.00e-02 2.50e+03 1.27e+02 ... (remaining 29237 not shown) Histogram of bond angle deviations from ideal: 73.50 - 85.91: 76 85.91 - 98.32: 2 98.32 - 110.73: 9439 110.73 - 123.14: 28478 123.14 - 135.55: 1639 Bond angle restraints: 39634 Sorted by residual: angle pdb=" N ASN M 74 " pdb=" CA ASN M 74 " pdb=" C ASN M 74 " ideal model delta sigma weight residual 111.36 122.04 -10.68 1.09e+00 8.42e-01 9.61e+01 angle pdb=" N TYR I 28 " pdb=" CA TYR I 28 " pdb=" C TYR I 28 " ideal model delta sigma weight residual 111.36 121.69 -10.33 1.09e+00 8.42e-01 8.97e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 125.32 -17.58 1.95e+00 2.62e-01 8.09e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.24 -14.40 1.91e+00 2.73e-01 5.65e+01 angle pdb=" O ASP Q 193 " pdb=" C ASP Q 193 " pdb=" N ILE Q 194 " ideal model delta sigma weight residual 122.09 129.78 -7.69 1.08e+00 8.57e-01 5.06e+01 ... (remaining 39629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 17001 35.13 - 70.26: 549 70.26 - 105.39: 47 105.39 - 140.52: 1 140.52 - 175.64: 1 Dihedral angle restraints: 17599 sinusoidal: 7370 harmonic: 10229 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 73.24 -175.64 1 2.00e+01 2.50e-03 4.79e+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 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" C MET M 173 " pdb=" N MET M 173 " pdb=" CA MET M 173 " pdb=" CB MET M 173 " ideal model delta harmonic sigma weight residual -122.60 -134.48 11.88 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 17596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4050 0.111 - 0.223: 202 0.223 - 0.334: 23 0.334 - 0.446: 7 0.446 - 0.557: 4 Chirality restraints: 4286 Sorted by residual: chirality pdb=" CA MET M 173 " pdb=" N MET M 173 " pdb=" C MET M 173 " pdb=" CB MET M 173 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" C23 970 Q 501 " pdb=" C14 970 Q 501 " pdb=" C22 970 Q 501 " pdb=" C24 970 Q 501 " both_signs ideal model delta sigma weight residual False 2.59 2.06 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA ASN M 74 " pdb=" N ASN M 74 " pdb=" C ASN M 74 " pdb=" CB ASN M 74 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.77e+00 ... (remaining 4283 not shown) Planarity restraints: 5096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.374 2.00e-02 2.50e+03 3.41e-01 1.45e+03 pdb=" C18 UQ J 402 " 0.358 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.402 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " 0.004 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.390 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.272 2.00e-02 2.50e+03 2.70e-01 9.09e+02 pdb=" C13 UQ J 402 " -0.225 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " -0.373 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " 0.010 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " 0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " 0.060 2.00e-02 2.50e+03 2.55e-01 8.15e+02 pdb=" C11 UQ J 402 " -0.113 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " 0.230 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " -0.436 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " 0.258 2.00e-02 2.50e+03 ... (remaining 5093 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 308 2.51 - 3.10: 21317 3.10 - 3.70: 48358 3.70 - 4.30: 75578 4.30 - 4.90: 116916 Nonbonded interactions: 262477 Sorted by model distance: nonbonded pdb=" NZ LYS M 298 " pdb=" O HOH M 901 " model vdw 1.907 2.520 nonbonded pdb=" OD1 ASP Q 137 " pdb=" OE2 GLU Q 148 " model vdw 1.940 3.040 nonbonded pdb=" NH1 ARG Q 333 " pdb=" O HOH Q 601 " model vdw 2.019 2.520 nonbonded pdb=" OE1 GLU M 83 " pdb=" O HOH M 902 " model vdw 2.033 2.440 nonbonded pdb=" OE2 GLU P 127 " pdb=" NZ LYS P 144 " model vdw 2.036 2.520 ... (remaining 262472 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 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 189 5.16 5 C 18107 2.51 5 N 4963 2.21 5 O 5992 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 7.920 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: 0.050 Extract box with map and model: 29.310 Check model and map are aligned: 0.430 Process input model: 88.970 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 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 : 0.009 0.303 29242 Z= 0.622 Angle : 0.927 17.575 39634 Z= 0.526 Chirality : 0.060 0.557 4286 Planarity : 0.010 0.341 5096 Dihedral : 16.442 175.645 11020 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.71 % Favored : 96.00 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 3.70 % 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: -0.05 (0.14), residues: 3502 helix: 0.65 (0.14), residues: 1353 sheet: 0.05 (0.26), residues: 363 loop : -0.51 (0.14), residues: 1786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 577 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 19 residues processed: 619 average time/residue: 1.9197 time to fit residues: 1347.7432 Evaluate side-chains 433 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 414 time to evaluate : 3.942 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 1.1207 time to fit residues: 7.9106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 456 GLN F 25 GLN F 31 GLN F 76 ASN I 25 GLN I 29 GLN J 323 HIS M 331 GLN M 336 ASN M 424 HIS M 540 ASN M 598 ASN N 13 GLN N 122 GLN N 123 GLN O 74 HIS P 236 ASN Q 147 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 29242 Z= 0.277 Angle : 0.627 10.543 39634 Z= 0.327 Chirality : 0.046 0.164 4286 Planarity : 0.005 0.058 5096 Dihedral : 8.654 174.130 4054 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.08 % Favored : 96.80 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.15 (0.14), residues: 3502 helix: 0.82 (0.14), residues: 1352 sheet: 0.24 (0.26), residues: 378 loop : -0.43 (0.14), residues: 1772 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 425 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 48 residues processed: 482 average time/residue: 1.8418 time to fit residues: 1015.7889 Evaluate side-chains 434 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 386 time to evaluate : 3.963 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 36 residues processed: 12 average time/residue: 0.9278 time to fit residues: 19.5296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 251 optimal weight: 0.0670 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN F 62 GLN J 323 HIS M 495 ASN M 669 ASN N 13 GLN Q 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 29242 Z= 0.253 Angle : 0.592 10.869 39634 Z= 0.310 Chirality : 0.045 0.158 4286 Planarity : 0.005 0.060 5096 Dihedral : 8.486 177.726 4054 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.86 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.21 (0.14), residues: 3502 helix: 0.87 (0.14), residues: 1353 sheet: 0.18 (0.26), residues: 380 loop : -0.37 (0.14), residues: 1769 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 398 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 51 residues processed: 458 average time/residue: 1.8644 time to fit residues: 975.7454 Evaluate side-chains 435 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 384 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 38 residues processed: 13 average time/residue: 0.8861 time to fit residues: 19.8095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 4.9990 chunk 235 optimal weight: 0.0980 chunk 162 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 314 optimal weight: 8.9990 chunk 333 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN F 31 GLN ** F 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN J 323 HIS M 669 ASN M 677 GLN N 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 29242 Z= 0.234 Angle : 0.572 10.815 39634 Z= 0.299 Chirality : 0.044 0.158 4286 Planarity : 0.005 0.060 5096 Dihedral : 8.369 176.684 4054 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.23 (0.14), residues: 3502 helix: 0.88 (0.14), residues: 1357 sheet: 0.18 (0.25), residues: 390 loop : -0.36 (0.14), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 395 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 56 residues processed: 451 average time/residue: 1.8902 time to fit residues: 978.0206 Evaluate side-chains 447 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 391 time to evaluate : 3.919 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 44 residues processed: 12 average time/residue: 1.0003 time to fit residues: 20.3564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 170 optimal weight: 0.1980 chunk 299 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS M 669 ASN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 29242 Z= 0.182 Angle : 0.532 10.691 39634 Z= 0.277 Chirality : 0.043 0.143 4286 Planarity : 0.004 0.059 5096 Dihedral : 8.108 176.011 4054 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.09 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.34 (0.14), residues: 3502 helix: 1.02 (0.14), residues: 1355 sheet: 0.27 (0.26), residues: 362 loop : -0.34 (0.14), residues: 1785 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 404 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 51 residues processed: 461 average time/residue: 1.8401 time to fit residues: 978.1764 Evaluate side-chains 443 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 392 time to evaluate : 3.745 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 42 residues processed: 9 average time/residue: 0.6469 time to fit residues: 13.7860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 333 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN F 62 GLN J 323 HIS M 669 ASN M 678 GLN N 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.117 29242 Z= 0.436 Angle : 0.714 11.130 39634 Z= 0.374 Chirality : 0.051 0.207 4286 Planarity : 0.006 0.071 5096 Dihedral : 8.684 176.916 4054 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.40 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.04 (0.14), residues: 3502 helix: 0.62 (0.14), residues: 1346 sheet: 0.16 (0.25), residues: 387 loop : -0.38 (0.14), residues: 1769 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 390 time to evaluate : 3.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 54 residues processed: 460 average time/residue: 1.8799 time to fit residues: 989.2233 Evaluate side-chains 431 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 377 time to evaluate : 3.705 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 45 residues processed: 9 average time/residue: 0.8488 time to fit residues: 14.9499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 188 optimal weight: 9.9990 chunk 280 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 332 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN F 31 GLN ** F 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 HIS J 323 HIS M 331 GLN M 678 GLN N 13 GLN P 236 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 29242 Z= 0.186 Angle : 0.546 10.680 39634 Z= 0.284 Chirality : 0.043 0.147 4286 Planarity : 0.005 0.064 5096 Dihedral : 8.212 179.884 4054 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.12 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.23 (0.14), residues: 3502 helix: 0.87 (0.14), residues: 1359 sheet: 0.23 (0.26), residues: 362 loop : -0.36 (0.14), residues: 1781 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 391 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 51 residues processed: 445 average time/residue: 1.8500 time to fit residues: 945.8790 Evaluate side-chains 438 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 387 time to evaluate : 3.595 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 41 residues processed: 10 average time/residue: 0.7755 time to fit residues: 14.9421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 100 optimal weight: 0.0970 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 211 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN F 31 GLN J 323 HIS M 331 GLN M 669 ASN M 678 GLN N 13 GLN N 123 GLN O 246 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 29242 Z= 0.151 Angle : 0.508 10.606 39634 Z= 0.262 Chirality : 0.041 0.139 4286 Planarity : 0.004 0.061 5096 Dihedral : 7.738 178.007 4054 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.89 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.40 (0.14), residues: 3502 helix: 1.09 (0.14), residues: 1357 sheet: 0.25 (0.25), residues: 377 loop : -0.32 (0.15), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 398 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 45 residues processed: 445 average time/residue: 1.8575 time to fit residues: 948.0457 Evaluate side-chains 437 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 392 time to evaluate : 3.633 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 6 average time/residue: 0.5995 time to fit residues: 9.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 5.9990 chunk 318 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 280 optimal weight: 0.7980 chunk 293 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS K 78 HIS M 669 ASN M 678 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29242 Z= 0.187 Angle : 0.539 12.205 39634 Z= 0.277 Chirality : 0.043 0.140 4286 Planarity : 0.004 0.063 5096 Dihedral : 7.758 179.393 4054 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.06 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.40 (0.14), residues: 3502 helix: 1.07 (0.14), residues: 1357 sheet: 0.26 (0.26), residues: 372 loop : -0.30 (0.14), residues: 1773 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 391 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 46 residues processed: 438 average time/residue: 1.8683 time to fit residues: 942.0520 Evaluate side-chains 435 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 389 time to evaluate : 3.702 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 40 residues processed: 6 average time/residue: 0.8647 time to fit residues: 11.7513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 227 optimal weight: 0.1980 chunk 343 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS M 331 GLN M 669 ASN M 678 GLN O 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 29242 Z= 0.247 Angle : 0.586 12.565 39634 Z= 0.303 Chirality : 0.045 0.172 4286 Planarity : 0.005 0.073 5096 Dihedral : 7.993 178.605 4054 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.86 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.32 (0.14), residues: 3502 helix: 0.96 (0.14), residues: 1354 sheet: 0.16 (0.25), residues: 392 loop : -0.28 (0.15), residues: 1756 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 390 time to evaluate : 3.952 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 44 residues processed: 434 average time/residue: 1.8546 time to fit residues: 922.8666 Evaluate side-chains 428 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 384 time to evaluate : 3.645 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 4 average time/residue: 0.8907 time to fit residues: 9.9973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 chunk 281 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS M 678 GLN N 13 GLN O 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.103530 restraints weight = 29879.756| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.07 r_work: 0.2950 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 29242 Z= 0.160 Angle : 0.522 12.420 39634 Z= 0.269 Chirality : 0.042 0.139 4286 Planarity : 0.004 0.061 5096 Dihedral : 7.712 179.210 4054 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.94 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.43 (0.14), residues: 3502 helix: 1.09 (0.14), residues: 1355 sheet: 0.26 (0.25), residues: 378 loop : -0.28 (0.15), residues: 1769 =============================================================================== Job complete usr+sys time: 15265.40 seconds wall clock time: 272 minutes 11.40 seconds (16331.40 seconds total)