Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 08:21:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4m_24831/04_2023/7s4m_24831_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4m_24831/04_2023/7s4m_24831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4m_24831/04_2023/7s4m_24831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4m_24831/04_2023/7s4m_24831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4m_24831/04_2023/7s4m_24831_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4m_24831/04_2023/7s4m_24831_trim_updated.pdb" } resolution = 2.42 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= 0.020 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: 6 Type Number sf(0) Gaussians Cu 6 5.60 5 P 12 5.49 5 S 72 5.16 5 C 14364 2.51 5 N 3498 2.21 5 O 3777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21729 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3026 Classifications: {'peptide': 388} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 361} Chain: "F" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1974 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain: "B" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1974 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain: "J" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1974 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain: "G" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1982 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "C" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1982 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1982 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "N" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3026 Classifications: {'peptide': 388} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 361} Chain: "I" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3026 Classifications: {'peptide': 388} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 361} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'D10': 1, 'HXG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'D10': 1, 'HXG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'D10': 1, 'HXG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' CU': 1, 'D10': 1, 'D12': 1, 'HXG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' CU': 1, 'D10': 1, 'D12': 1, 'HXG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' CU': 1, 'D10': 1, 'D12': 1, 'HXG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "A" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 11.05, per 1000 atoms: 0.51 Number of scatterers: 21729 At special positions: 0 Unit cell: (110.24, 107.64, 119.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 6 28.99 S 72 16.00 P 12 15.00 O 3777 8.00 N 3498 7.00 C 14364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 8.40 Conformation dependent library (CDL) restraints added in 3.1 seconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4878 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 21 sheets defined 49.3% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 181 through 205 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 228 through 252 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.945A pdb=" N ALA A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 49 removed outlier: 4.681A pdb=" N ALA F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY F 40 " --> pdb=" O PHE F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 64 through 88 Proline residue: F 70 - end of helix removed outlier: 4.342A pdb=" N THR F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 Processing helix chain 'F' and resid 121 through 124 No H-bonds generated for 'chain 'F' and resid 121 through 124' Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 146 through 173 removed outlier: 3.940A pdb=" N SER F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE F 161 " --> pdb=" O TRP F 157 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR F 162 " --> pdb=" O GLY F 158 " (cutoff:3.500A) Proline residue: F 163 - end of helix Proline residue: F 167 - end of helix removed outlier: 5.253A pdb=" N ALA F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 192 Processing helix chain 'F' and resid 217 through 243 removed outlier: 3.815A pdb=" N MET F 230 " --> pdb=" O GLY F 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 49 removed outlier: 4.566A pdb=" N ALA B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLY B 40 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 65 through 88 Proline residue: B 70 - end of helix removed outlier: 4.178A pdb=" N THR B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 121 through 124 No H-bonds generated for 'chain 'B' and resid 121 through 124' Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 146 through 169 removed outlier: 3.791A pdb=" N SER B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 161 " --> pdb=" O TRP B 157 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Proline residue: B 163 - end of helix Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 200 through 203 Processing helix chain 'B' and resid 217 through 243 removed outlier: 4.561A pdb=" N MET B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N MET B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 49 removed outlier: 4.612A pdb=" N ALA J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY J 40 " --> pdb=" O PHE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 59 No H-bonds generated for 'chain 'J' and resid 57 through 59' Processing helix chain 'J' and resid 65 through 88 Proline residue: J 70 - end of helix removed outlier: 4.374A pdb=" N THR J 75 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE J 76 " --> pdb=" O LEU J 72 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 111 Processing helix chain 'J' and resid 121 through 124 No H-bonds generated for 'chain 'J' and resid 121 through 124' Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 146 through 173 removed outlier: 3.614A pdb=" N SER J 154 " --> pdb=" O ALA J 150 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE J 161 " --> pdb=" O TRP J 157 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR J 162 " --> pdb=" O GLY J 158 " (cutoff:3.500A) Proline residue: J 163 - end of helix Proline residue: J 167 - end of helix removed outlier: 5.099A pdb=" N ALA J 171 " --> pdb=" O PRO J 167 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 192 Processing helix chain 'J' and resid 217 through 243 removed outlier: 4.311A pdb=" N MET J 230 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N MET J 231 " --> pdb=" O PHE J 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL J 232 " --> pdb=" O VAL J 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 45 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 63 through 86 removed outlier: 3.796A pdb=" N ILE G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Proline residue: G 71 - end of helix Processing helix chain 'G' and resid 92 through 94 No H-bonds generated for 'chain 'G' and resid 92 through 94' Processing helix chain 'G' and resid 97 through 122 Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.762A pdb=" N GLY G 130 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 153 through 171 Processing helix chain 'G' and resid 173 through 176 No H-bonds generated for 'chain 'G' and resid 173 through 176' Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 195 through 205 removed outlier: 4.403A pdb=" N ASN G 200 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU G 201 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP G 202 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 245 removed outlier: 4.824A pdb=" N GLY G 220 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE G 223 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE G 224 " --> pdb=" O PHE G 221 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP G 226 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 251 No H-bonds generated for 'chain 'G' and resid 248 through 251' Processing helix chain 'C' and resid 22 through 45 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 63 through 86 removed outlier: 3.700A pdb=" N ILE C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 97 through 122 Processing helix chain 'C' and resid 124 through 132 removed outlier: 3.925A pdb=" N GLY C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 153 through 171 Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.664A pdb=" N GLY C 198 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TRP C 202 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 203 " --> pdb=" O ASN C 200 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS C 204 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 245 removed outlier: 3.735A pdb=" N GLY C 220 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 223 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE C 224 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP C 226 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 251 No H-bonds generated for 'chain 'C' and resid 248 through 251' Processing helix chain 'D' and resid 5 through 18 removed outlier: 3.573A pdb=" N UNK D 11 " --> pdb=" O UNK D 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 45 Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'K' and resid 63 through 86 removed outlier: 3.850A pdb=" N ILE K 70 " --> pdb=" O LEU K 66 " (cutoff:3.500A) Proline residue: K 71 - end of helix Processing helix chain 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'K' and resid 97 through 122 Processing helix chain 'K' and resid 124 through 132 removed outlier: 3.707A pdb=" N GLY K 130 " --> pdb=" O THR K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 149 Processing helix chain 'K' and resid 153 through 171 Processing helix chain 'K' and resid 173 through 176 No H-bonds generated for 'chain 'K' and resid 173 through 176' Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 191 through 201 Proline residue: K 195 - end of helix removed outlier: 5.229A pdb=" N GLY K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU K 199 " --> pdb=" O PRO K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 245 removed outlier: 3.994A pdb=" N MET K 227 " --> pdb=" O PHE K 223 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA K 228 " --> pdb=" O PHE K 224 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU K 229 " --> pdb=" O GLY K 225 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY K 230 " --> pdb=" O TRP K 226 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL K 231 " --> pdb=" O MET K 227 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N PHE K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY K 233 " --> pdb=" O LEU K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 252 removed outlier: 3.513A pdb=" N LYS K 252 " --> pdb=" O LYS K 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 248 through 252' Processing helix chain 'N' and resid 8 through 19 Processing helix chain 'H' and resid 5 through 18 removed outlier: 3.807A pdb=" N UNK H 11 " --> pdb=" O UNK H 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 36 through 40 Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 181 through 205 Proline residue: E 190 - end of helix Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 228 through 252 Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 378 through 382 removed outlier: 3.944A pdb=" N ALA E 381 " --> pdb=" O SER E 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 33 No H-bonds generated for 'chain 'I' and resid 31 through 33' Processing helix chain 'I' and resid 36 through 40 Processing helix chain 'I' and resid 159 through 161 No H-bonds generated for 'chain 'I' and resid 159 through 161' Processing helix chain 'I' and resid 181 through 205 Proline residue: I 190 - end of helix Processing helix chain 'I' and resid 208 through 216 Processing helix chain 'I' and resid 228 through 252 Processing helix chain 'I' and resid 370 through 374 Processing helix chain 'I' and resid 377 through 382 removed outlier: 3.944A pdb=" N ALA I 381 " --> pdb=" O SER I 378 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 3.556A pdb=" N ALA A 98 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG A 125 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG A 96 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 54 through 56 removed outlier: 7.864A pdb=" N VAL A 55 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A 154 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 137 through 140 Processing sheet with id= D, first strand: chain 'A' and resid 285 through 288 Processing sheet with id= E, first strand: chain 'A' and resid 300 through 302 removed outlier: 6.861A pdb=" N ILE A 411 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL A 295 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS A 413 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.815A pdb=" N PHE A 393 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR A 319 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 391 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 175 through 177 Processing sheet with id= H, first strand: chain 'B' and resid 175 through 177 Processing sheet with id= I, first strand: chain 'J' and resid 175 through 177 Processing sheet with id= J, first strand: chain 'E' and resid 43 through 46 removed outlier: 3.557A pdb=" N ALA E 98 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG E 125 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG E 96 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 54 through 56 removed outlier: 7.863A pdb=" N VAL E 55 " --> pdb=" O TRP E 152 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU E 154 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 137 through 140 Processing sheet with id= M, first strand: chain 'E' and resid 285 through 288 Processing sheet with id= N, first strand: chain 'E' and resid 300 through 302 removed outlier: 6.862A pdb=" N ILE E 411 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL E 295 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS E 413 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 325 through 327 removed outlier: 6.815A pdb=" N PHE E 393 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR E 319 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU E 391 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 43 through 46 removed outlier: 3.557A pdb=" N ALA I 98 " --> pdb=" O ASN I 123 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG I 125 " --> pdb=" O ARG I 96 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG I 96 " --> pdb=" O ARG I 125 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 54 through 56 removed outlier: 7.864A pdb=" N VAL I 55 " --> pdb=" O TRP I 152 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU I 154 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 137 through 140 Processing sheet with id= S, first strand: chain 'I' and resid 285 through 288 Processing sheet with id= T, first strand: chain 'I' and resid 300 through 302 removed outlier: 6.862A pdb=" N ILE I 411 " --> pdb=" O TYR I 293 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL I 295 " --> pdb=" O ILE I 411 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS I 413 " --> pdb=" O VAL I 295 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 325 through 327 removed outlier: 6.815A pdb=" N PHE I 393 " --> pdb=" O GLY I 317 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR I 319 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU I 391 " --> pdb=" O TYR I 319 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.91 Time building geometry restraints manager: 9.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3514 1.32 - 1.45: 6467 1.45 - 1.57: 12183 1.57 - 1.69: 36 1.69 - 1.82: 138 Bond restraints: 22338 Sorted by residual: bond pdb=" N VAL A 295 " pdb=" CA VAL A 295 " ideal model delta sigma weight residual 1.456 1.494 -0.037 8.70e-03 1.32e+04 1.85e+01 bond pdb=" N VAL I 295 " pdb=" CA VAL I 295 " ideal model delta sigma weight residual 1.456 1.494 -0.037 8.70e-03 1.32e+04 1.84e+01 bond pdb=" N VAL E 295 " pdb=" CA VAL E 295 " ideal model delta sigma weight residual 1.456 1.493 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" N PHE K 208 " pdb=" CA PHE K 208 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.09e+01 bond pdb=" N ILE K 194 " pdb=" CA ILE K 194 " ideal model delta sigma weight residual 1.463 1.502 -0.039 1.20e-02 6.94e+03 1.04e+01 ... (remaining 22333 not shown) Histogram of bond angle deviations from ideal: 97.11 - 105.11: 445 105.11 - 113.12: 11957 113.12 - 121.13: 12107 121.13 - 129.13: 5614 129.13 - 137.14: 315 Bond angle restraints: 30438 Sorted by residual: angle pdb=" C PHE K 208 " pdb=" CA PHE K 208 " pdb=" CB PHE K 208 " ideal model delta sigma weight residual 109.65 124.12 -14.47 1.71e+00 3.42e-01 7.16e+01 angle pdb=" C PRO K 195 " pdb=" CA PRO K 195 " pdb=" CB PRO K 195 " ideal model delta sigma weight residual 111.56 99.19 12.37 1.65e+00 3.67e-01 5.62e+01 angle pdb=" N PRO K 195 " pdb=" CA PRO K 195 " pdb=" CB PRO K 195 " ideal model delta sigma weight residual 103.25 97.11 6.14 1.05e+00 9.07e-01 3.42e+01 angle pdb=" N MET K 209 " pdb=" CA MET K 209 " pdb=" C MET K 209 " ideal model delta sigma weight residual 112.59 119.42 -6.83 1.22e+00 6.72e-01 3.14e+01 angle pdb=" N LEU E 377 " pdb=" CA LEU E 377 " pdb=" C LEU E 377 " ideal model delta sigma weight residual 113.23 106.63 6.60 1.24e+00 6.50e-01 2.83e+01 ... (remaining 30433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.05: 11696 28.05 - 56.09: 759 56.09 - 84.14: 108 84.14 - 112.18: 21 112.18 - 140.23: 10 Dihedral angle restraints: 12594 sinusoidal: 4959 harmonic: 7635 Sorted by residual: dihedral pdb=" CA ASP E 226 " pdb=" C ASP E 226 " pdb=" N ASP E 227 " pdb=" CA ASP E 227 " ideal model delta harmonic sigma weight residual 180.00 54.22 125.78 0 5.00e+00 4.00e-02 6.33e+02 dihedral pdb=" CA ASP A 226 " pdb=" C ASP A 226 " pdb=" N ASP A 227 " pdb=" CA ASP A 227 " ideal model delta harmonic sigma weight residual 180.00 54.27 125.73 0 5.00e+00 4.00e-02 6.32e+02 dihedral pdb=" CA ASP I 226 " pdb=" C ASP I 226 " pdb=" N ASP I 227 " pdb=" CA ASP I 227 " ideal model delta harmonic sigma weight residual 180.00 54.28 125.72 0 5.00e+00 4.00e-02 6.32e+02 ... (remaining 12591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2543 0.061 - 0.121: 635 0.121 - 0.182: 89 0.182 - 0.242: 27 0.242 - 0.303: 3 Chirality restraints: 3297 Sorted by residual: chirality pdb=" CA PHE K 208 " pdb=" N PHE K 208 " pdb=" C PHE K 208 " pdb=" CB PHE K 208 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB VAL G 92 " pdb=" CA VAL G 92 " pdb=" CG1 VAL G 92 " pdb=" CG2 VAL G 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE C 194 " pdb=" CA ILE C 194 " pdb=" CG1 ILE C 194 " pdb=" CG2 ILE C 194 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3294 not shown) Planarity restraints: 3759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 194 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 195 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 195 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 195 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 37 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ALA J 37 " 0.068 2.00e-02 2.50e+03 pdb=" O ALA J 37 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL J 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 37 " -0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ALA B 37 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA B 37 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL B 38 " -0.023 2.00e-02 2.50e+03 ... (remaining 3756 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 263 2.59 - 3.17: 18874 3.17 - 3.75: 37309 3.75 - 4.32: 53831 4.32 - 4.90: 87217 Nonbonded interactions: 197494 Sorted by model distance: nonbonded pdb=" O PRO C 195 " pdb=" O HOH C 401 " model vdw 2.015 2.440 nonbonded pdb=" NE2 HIS C 146 " pdb="CU CU C 301 " model vdw 2.026 2.320 nonbonded pdb=" OD2 ASP K 129 " pdb="CU CU K 301 " model vdw 2.029 2.240 nonbonded pdb=" NE2 HIS K 146 " pdb="CU CU K 301 " model vdw 2.032 2.320 nonbonded pdb=" NE2 HIS G 146 " pdb="CU CU G 301 " model vdw 2.047 2.320 ... (remaining 197489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' } 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.890 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 53.360 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.220 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: 0.000 Load rotamer database and sin/cos tables:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 22338 Z= 0.460 Angle : 0.934 14.842 30438 Z= 0.552 Chirality : 0.055 0.303 3297 Planarity : 0.005 0.117 3759 Dihedral : 18.769 140.225 7716 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.54 % Favored : 94.04 % Rotamer Outliers : 6.06 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.17 (0.17), residues: 2601 helix: 1.03 (0.15), residues: 1248 sheet: -0.25 (0.27), residues: 390 loop : -1.57 (0.21), residues: 963 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 224 time to evaluate : 2.952 Fit side-chains outliers start: 132 outliers final: 33 residues processed: 327 average time/residue: 1.4049 time to fit residues: 521.5961 Evaluate side-chains 175 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 29 residues processed: 6 average time/residue: 0.2647 time to fit residues: 5.9933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN F 164 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 243 HIS E 387 GLN I 387 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 22338 Z= 0.268 Angle : 0.657 11.593 30438 Z= 0.345 Chirality : 0.046 0.205 3297 Planarity : 0.006 0.089 3759 Dihedral : 11.691 136.108 3120 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.58 % Favored : 95.19 % Rotamer Outliers : 5.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.22 (0.17), residues: 2601 helix: 1.03 (0.15), residues: 1230 sheet: 0.14 (0.29), residues: 336 loop : -1.71 (0.19), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 180 time to evaluate : 2.404 Fit side-chains outliers start: 125 outliers final: 60 residues processed: 288 average time/residue: 1.1269 time to fit residues: 381.4203 Evaluate side-chains 196 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 136 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 55 residues processed: 6 average time/residue: 0.2634 time to fit residues: 5.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 197 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 237 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 139 ASN A 328 ASN F 87 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 139 ASN ** I 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 22338 Z= 0.332 Angle : 0.658 9.619 30438 Z= 0.343 Chirality : 0.047 0.201 3297 Planarity : 0.006 0.084 3759 Dihedral : 10.821 138.835 3120 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Rotamer Outliers : 5.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.17), residues: 2601 helix: 0.84 (0.15), residues: 1227 sheet: -0.17 (0.29), residues: 342 loop : -1.69 (0.19), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 139 time to evaluate : 2.507 Fit side-chains revert: symmetry clash outliers start: 129 outliers final: 74 residues processed: 255 average time/residue: 1.1035 time to fit residues: 331.8082 Evaluate side-chains 210 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 136 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 71 residues processed: 3 average time/residue: 0.1902 time to fit residues: 4.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 164 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 139 ASN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5743 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 22338 Z= 0.268 Angle : 0.614 9.576 30438 Z= 0.320 Chirality : 0.045 0.192 3297 Planarity : 0.005 0.090 3759 Dihedral : 10.432 137.636 3120 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 5.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.17), residues: 2601 helix: 0.85 (0.15), residues: 1200 sheet: -0.22 (0.27), residues: 366 loop : -1.62 (0.19), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 149 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 76 residues processed: 260 average time/residue: 0.9737 time to fit residues: 302.9701 Evaluate side-chains 217 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 141 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 72 residues processed: 4 average time/residue: 0.2250 time to fit residues: 4.9084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 22338 Z= 0.300 Angle : 0.627 11.102 30438 Z= 0.326 Chirality : 0.046 0.182 3297 Planarity : 0.005 0.094 3759 Dihedral : 10.049 136.879 3120 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 5.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.49 (0.17), residues: 2601 helix: 0.80 (0.15), residues: 1200 sheet: -0.20 (0.27), residues: 360 loop : -1.70 (0.19), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 149 time to evaluate : 2.387 Fit side-chains revert: symmetry clash outliers start: 128 outliers final: 88 residues processed: 262 average time/residue: 1.0609 time to fit residues: 330.8153 Evaluate side-chains 232 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 144 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 77 residues processed: 11 average time/residue: 0.4101 time to fit residues: 9.8338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 22338 Z= 0.267 Angle : 0.612 13.121 30438 Z= 0.317 Chirality : 0.045 0.180 3297 Planarity : 0.005 0.092 3759 Dihedral : 9.623 135.680 3120 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 5.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.54 (0.17), residues: 2601 helix: 0.76 (0.15), residues: 1236 sheet: -0.40 (0.26), residues: 381 loop : -1.77 (0.19), residues: 984 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 144 time to evaluate : 2.217 Fit side-chains outliers start: 125 outliers final: 85 residues processed: 258 average time/residue: 1.0109 time to fit residues: 311.7393 Evaluate side-chains 225 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 140 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 82 residues processed: 3 average time/residue: 0.5968 time to fit residues: 5.6225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 184 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 218 HIS ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 22338 Z= 0.267 Angle : 0.619 17.079 30438 Z= 0.318 Chirality : 0.045 0.185 3297 Planarity : 0.005 0.088 3759 Dihedral : 9.354 134.714 3120 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 5.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.52 (0.17), residues: 2601 helix: 0.76 (0.15), residues: 1248 sheet: -0.40 (0.26), residues: 381 loop : -1.77 (0.19), residues: 972 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 144 time to evaluate : 2.496 Fit side-chains revert: symmetry clash outliers start: 121 outliers final: 86 residues processed: 255 average time/residue: 0.9998 time to fit residues: 306.4021 Evaluate side-chains 224 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 138 time to evaluate : 2.236 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 82 residues processed: 4 average time/residue: 0.2317 time to fit residues: 4.8865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 139 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 22338 Z= 0.198 Angle : 0.591 9.571 30438 Z= 0.303 Chirality : 0.043 0.172 3297 Planarity : 0.005 0.086 3759 Dihedral : 9.042 132.627 3120 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 4.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.78 % Twisted General : 0.04 % 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 (0.17), residues: 2601 helix: 0.93 (0.15), residues: 1230 sheet: 0.03 (0.27), residues: 360 loop : -1.75 (0.19), residues: 1011 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 147 time to evaluate : 2.353 Fit side-chains revert: symmetry clash outliers start: 108 outliers final: 82 residues processed: 251 average time/residue: 1.0052 time to fit residues: 302.0487 Evaluate side-chains 221 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 139 time to evaluate : 2.328 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 80 residues processed: 2 average time/residue: 0.6596 time to fit residues: 4.6460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 141 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 184 optimal weight: 30.0000 chunk 71 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 22338 Z= 0.341 Angle : 0.660 15.861 30438 Z= 0.338 Chirality : 0.046 0.183 3297 Planarity : 0.006 0.088 3759 Dihedral : 9.180 132.810 3120 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 4.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.59 (0.17), residues: 2601 helix: 0.72 (0.15), residues: 1215 sheet: -0.39 (0.26), residues: 381 loop : -1.77 (0.19), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 146 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 83 residues processed: 247 average time/residue: 1.1005 time to fit residues: 327.5956 Evaluate side-chains 223 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 140 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 80 residues processed: 3 average time/residue: 0.9658 time to fit residues: 6.5104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 22338 Z= 0.299 Angle : 0.640 14.072 30438 Z= 0.328 Chirality : 0.045 0.167 3297 Planarity : 0.006 0.096 3759 Dihedral : 9.139 131.495 3120 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.61 (0.17), residues: 2601 helix: 0.73 (0.15), residues: 1215 sheet: -0.42 (0.26), residues: 381 loop : -1.80 (0.19), residues: 1005 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 137 time to evaluate : 2.392 Fit side-chains revert: symmetry clash outliers start: 91 outliers final: 83 residues processed: 226 average time/residue: 1.0010 time to fit residues: 271.8106 Evaluate side-chains 219 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 136 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 82 residues processed: 1 average time/residue: 1.1633 time to fit residues: 4.6151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 212 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 139 ASN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.165087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128319 restraints weight = 21929.879| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.65 r_work: 0.3491 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22338 Z= 0.204 Angle : 0.594 10.233 30438 Z= 0.304 Chirality : 0.043 0.164 3297 Planarity : 0.005 0.080 3759 Dihedral : 8.846 128.220 3120 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.48 % 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: -0.44 (0.17), residues: 2601 helix: 0.85 (0.15), residues: 1236 sheet: -0.24 (0.27), residues: 381 loop : -1.80 (0.19), residues: 984 =============================================================================== Job complete usr+sys time: 6391.79 seconds wall clock time: 115 minutes 1.16 seconds (6901.16 seconds total)