Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 17 06:30:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/05_2023/7s4k_24829_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/05_2023/7s4k_24829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/05_2023/7s4k_24829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/05_2023/7s4k_24829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/05_2023/7s4k_24829_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/05_2023/7s4k_24829_trim_updated.pdb" } resolution = 2.36 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19395 atoms to isotropic. 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 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15030 2.51 5 N 3417 2.21 5 O 4004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 22589 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 284 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 273 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 284 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 11.83, per 1000 atoms: 0.52 Number of scatterers: 22589 At special positions: 0 Unit cell: (107.194, 107.667, 118.056, 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 9 28.99 S 93 16.00 P 36 15.00 O 4004 8.00 N 3417 7.00 C 15030 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: 9.98 Conformation dependent library (CDL) restraints added in 3.3 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 24 sheets defined 48.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 185 through 207 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 232 through 256 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.523A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.962A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 124 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 208 through 232 Proline residue: C 217 - end of helix removed outlier: 3.636A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.653A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 4.372A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.442A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.867A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 141 through 168 removed outlier: 4.213A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.789A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.963A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 88 Processing helix chain 'G' and resid 90 through 113 Processing helix chain 'G' and resid 124 through 149 Processing helix chain 'G' and resid 151 through 162 Processing helix chain 'G' and resid 171 through 177 Processing helix chain 'G' and resid 180 through 198 Processing helix chain 'G' and resid 208 through 232 Proline residue: G 217 - end of helix removed outlier: 3.636A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.653A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 4.372A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.963A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 88 Processing helix chain 'K' and resid 90 through 113 Processing helix chain 'K' and resid 124 through 149 Processing helix chain 'K' and resid 151 through 162 Processing helix chain 'K' and resid 171 through 177 Processing helix chain 'K' and resid 180 through 198 Processing helix chain 'K' and resid 208 through 232 Proline residue: K 217 - end of helix removed outlier: 3.636A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.653A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 4.371A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 207 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 232 through 256 Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.522A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'I' and resid 185 through 207 Processing helix chain 'I' and resid 213 through 220 Processing helix chain 'I' and resid 232 through 256 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 369 through 373 Processing helix chain 'I' and resid 376 through 381 removed outlier: 3.523A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 44 Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 59 through 83 Proline residue: F 65 - end of helix removed outlier: 4.442A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.868A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 Processing helix chain 'F' and resid 116 through 119 No H-bonds generated for 'chain 'F' and resid 116 through 119' Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 141 through 168 removed outlier: 4.213A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Proline residue: F 166 - end of helix Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 212 through 238 removed outlier: 3.789A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 59 through 83 Proline residue: J 65 - end of helix removed outlier: 4.443A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.867A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 106 Processing helix chain 'J' and resid 116 through 119 No H-bonds generated for 'chain 'J' and resid 116 through 119' Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 141 through 168 removed outlier: 4.212A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 212 through 238 removed outlier: 3.788A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.723A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 removed outlier: 8.342A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR A 158 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 141 through 144 Processing sheet with id= D, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'A' and resid 282 through 286 Processing sheet with id= F, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.536A pdb=" N ILE A 410 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.668A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= I, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.722A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 58 through 60 removed outlier: 8.342A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 141 through 144 Processing sheet with id= L, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'E' and resid 282 through 286 Processing sheet with id= N, first strand: chain 'E' and resid 298 through 300 removed outlier: 6.537A pdb=" N ILE E 410 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.668A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.723A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 58 through 60 removed outlier: 8.342A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR I 158 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 141 through 144 Processing sheet with id= S, first strand: chain 'I' and resid 169 through 171 Processing sheet with id= T, first strand: chain 'I' and resid 282 through 286 Processing sheet with id= U, first strand: chain 'I' and resid 298 through 300 removed outlier: 6.536A pdb=" N ILE I 410 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.668A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 170 through 173 Processing sheet with id= X, first strand: chain 'J' and resid 170 through 173 1023 hydrogen bonds defined for protein. 2808 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: 10.54 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: 3292 1.32 - 1.44: 6810 1.44 - 1.56: 12679 1.56 - 1.69: 166 1.69 - 1.81: 180 Bond restraints: 23127 Sorted by residual: bond pdb=" CB PLC J 303 " pdb=" O3 PLC J 303 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" CB PLC C 310 " pdb=" O3 PLC C 310 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" CB PLC G 301 " pdb=" O3 PLC G 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PLC B 301 " pdb=" O3 PLC B 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CB PLC F 302 " pdb=" O3 PLC F 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 4.00e+01 ... (remaining 23122 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.36: 1087 107.36 - 115.09: 13537 115.09 - 122.83: 14613 122.83 - 130.56: 1888 130.56 - 138.30: 168 Bond angle restraints: 31293 Sorted by residual: angle pdb=" C9' PLC F 302 " pdb=" CA' PLC F 302 " pdb=" CB' PLC F 302 " ideal model delta sigma weight residual 112.96 134.60 -21.64 3.00e+00 1.11e-01 5.20e+01 angle pdb=" C9' PLC B 301 " pdb=" CA' PLC B 301 " pdb=" CB' PLC B 301 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" C9' PLC J 305 " pdb=" CA' PLC J 305 " pdb=" CB' PLC J 305 " ideal model delta sigma weight residual 112.96 134.53 -21.57 3.00e+00 1.11e-01 5.17e+01 angle pdb=" CA HIS G 173 " pdb=" CB HIS G 173 " pdb=" CG HIS G 173 " ideal model delta sigma weight residual 113.80 120.87 -7.07 1.00e+00 1.00e+00 5.00e+01 angle pdb=" CA HIS K 173 " pdb=" CB HIS K 173 " pdb=" CG HIS K 173 " ideal model delta sigma weight residual 113.80 120.85 -7.05 1.00e+00 1.00e+00 4.97e+01 ... (remaining 31288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.45: 12232 30.45 - 60.91: 822 60.91 - 91.36: 50 91.36 - 121.82: 6 121.82 - 152.27: 9 Dihedral angle restraints: 13119 sinusoidal: 5667 harmonic: 7452 Sorted by residual: dihedral pdb=" CA GLN C 276 " pdb=" C GLN C 276 " pdb=" N SER C 277 " pdb=" CA SER C 277 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLN G 276 " pdb=" C GLN G 276 " pdb=" N SER G 277 " pdb=" CA SER G 277 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLN K 276 " pdb=" C GLN K 276 " pdb=" N SER K 277 " pdb=" CA SER K 277 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 13116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2340 0.048 - 0.096: 613 0.096 - 0.145: 199 0.145 - 0.193: 32 0.193 - 0.241: 23 Chirality restraints: 3207 Sorted by residual: chirality pdb=" C2 PLC K 305 " pdb=" C1 PLC K 305 " pdb=" C3 PLC K 305 " pdb=" O2 PLC K 305 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 PLC G 307 " pdb=" C1 PLC G 307 " pdb=" C3 PLC G 307 " pdb=" O2 PLC G 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2 PLC C 307 " pdb=" C1 PLC C 307 " pdb=" C3 PLC C 307 " pdb=" O2 PLC C 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 160 " 0.030 2.00e-02 2.50e+03 2.70e-02 1.09e+01 pdb=" CG HIS G 160 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS G 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS G 160 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 160 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS G 160 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 160 " -0.029 2.00e-02 2.50e+03 2.69e-02 1.09e+01 pdb=" CG HIS C 160 " 0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS C 160 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS C 160 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 160 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 160 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 160 " 0.029 2.00e-02 2.50e+03 2.68e-02 1.08e+01 pdb=" CG HIS K 160 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS K 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS K 160 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS K 160 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS K 160 " 0.021 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 21 2.14 - 2.83: 7106 2.83 - 3.52: 32076 3.52 - 4.21: 62137 4.21 - 4.90: 105761 Nonbonded interactions: 207101 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 301 " model vdw 1.448 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.448 2.320 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.448 2.320 nonbonded pdb=" ND1 HIS E 48 " pdb="CU CU E 502 " model vdw 1.975 2.320 nonbonded pdb=" ND1 HIS A 48 " pdb="CU CU A 502 " model vdw 1.976 2.320 ... (remaining 207096 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' and resid 7 through 247) selection = (chain 'F' and resid 7 through 247) selection = (chain 'J' and resid 7 through 247) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 305)) selection = (chain 'G' and (resid 45 through 280 or resid 305)) selection = (chain 'K' and (resid 45 through 280 or resid 305)) } 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.020 Extract box with map and model: 18.430 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 57.630 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.150 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 0.127 23127 Z= 0.551 Angle : 1.049 21.643 31293 Z= 0.524 Chirality : 0.052 0.241 3207 Planarity : 0.005 0.041 3732 Dihedral : 18.911 152.273 8361 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.37 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.71 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1185 sheet: 1.09 (0.31), residues: 333 loop : -0.29 (0.20), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 228 time to evaluate : 2.647 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 40 residues processed: 286 average time/residue: 1.5963 time to fit residues: 513.2574 Evaluate side-chains 255 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 2.367 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 3 average time/residue: 0.2529 time to fit residues: 4.4979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 118 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 23127 Z= 0.282 Angle : 0.604 5.966 31293 Z= 0.311 Chirality : 0.047 0.276 3207 Planarity : 0.005 0.043 3732 Dihedral : 15.668 142.971 3726 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.26 % Favored : 95.39 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.79 (0.17), residues: 2559 helix: 1.10 (0.15), residues: 1206 sheet: 0.98 (0.29), residues: 342 loop : -0.23 (0.20), residues: 1011 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 226 time to evaluate : 2.711 Fit side-chains outliers start: 87 outliers final: 54 residues processed: 294 average time/residue: 1.5192 time to fit residues: 505.4289 Evaluate side-chains 272 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 218 time to evaluate : 2.672 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 48 residues processed: 7 average time/residue: 0.6714 time to fit residues: 9.3856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 250 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 23127 Z= 0.355 Angle : 0.613 6.222 31293 Z= 0.321 Chirality : 0.048 0.226 3207 Planarity : 0.005 0.046 3732 Dihedral : 15.039 142.905 3726 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.10 % Favored : 95.55 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.69 (0.17), residues: 2559 helix: 1.01 (0.15), residues: 1215 sheet: 0.89 (0.27), residues: 372 loop : -0.31 (0.20), residues: 972 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 216 time to evaluate : 2.636 Fit side-chains outliers start: 84 outliers final: 56 residues processed: 285 average time/residue: 1.5130 time to fit residues: 489.5097 Evaluate side-chains 266 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 210 time to evaluate : 2.735 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 49 residues processed: 9 average time/residue: 0.5038 time to fit residues: 9.9346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 23127 Z= 0.301 Angle : 0.587 6.144 31293 Z= 0.307 Chirality : 0.046 0.218 3207 Planarity : 0.005 0.045 3732 Dihedral : 14.555 135.926 3726 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.34 % Favored : 95.35 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.74 (0.17), residues: 2559 helix: 1.04 (0.15), residues: 1215 sheet: 0.88 (0.27), residues: 372 loop : -0.25 (0.20), residues: 972 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 220 time to evaluate : 2.638 Fit side-chains outliers start: 86 outliers final: 55 residues processed: 288 average time/residue: 1.5467 time to fit residues: 503.0131 Evaluate side-chains 263 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 208 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 47 residues processed: 10 average time/residue: 0.8276 time to fit residues: 13.0883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23127 Z= 0.190 Angle : 0.540 6.054 31293 Z= 0.281 Chirality : 0.044 0.185 3207 Planarity : 0.004 0.043 3732 Dihedral : 13.981 125.745 3726 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.39 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.85 (0.17), residues: 2559 helix: 1.19 (0.15), residues: 1200 sheet: 0.76 (0.27), residues: 390 loop : -0.19 (0.20), residues: 969 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 224 time to evaluate : 2.660 Fit side-chains outliers start: 75 outliers final: 55 residues processed: 287 average time/residue: 1.5746 time to fit residues: 511.8124 Evaluate side-chains 269 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 214 time to evaluate : 2.604 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 47 residues processed: 9 average time/residue: 0.6698 time to fit residues: 11.0847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 161 GLN K 161 GLN I 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 23127 Z= 0.228 Angle : 0.552 6.239 31293 Z= 0.288 Chirality : 0.045 0.197 3207 Planarity : 0.004 0.044 3732 Dihedral : 13.702 122.849 3726 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.89 (0.17), residues: 2559 helix: 1.17 (0.15), residues: 1203 sheet: 0.97 (0.27), residues: 372 loop : -0.18 (0.20), residues: 984 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 214 time to evaluate : 2.572 Fit side-chains outliers start: 79 outliers final: 56 residues processed: 275 average time/residue: 1.4962 time to fit residues: 467.1957 Evaluate side-chains 267 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 46 residues processed: 11 average time/residue: 0.5107 time to fit residues: 11.0792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 161 GLN G 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 23127 Z= 0.318 Angle : 0.595 6.974 31293 Z= 0.312 Chirality : 0.047 0.218 3207 Planarity : 0.005 0.046 3732 Dihedral : 13.756 125.319 3726 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.38 % Favored : 95.43 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.78 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1218 sheet: 0.88 (0.27), residues: 372 loop : -0.16 (0.20), residues: 969 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 214 time to evaluate : 2.670 Fit side-chains outliers start: 71 outliers final: 55 residues processed: 269 average time/residue: 1.5560 time to fit residues: 475.6390 Evaluate side-chains 264 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 209 time to evaluate : 2.704 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 43 residues processed: 13 average time/residue: 0.5950 time to fit residues: 13.6738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 0.0020 chunk 193 optimal weight: 6.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN I 108 GLN F 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 23127 Z= 0.148 Angle : 0.527 6.684 31293 Z= 0.274 Chirality : 0.044 0.186 3207 Planarity : 0.004 0.043 3732 Dihedral : 13.144 117.410 3726 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.73 % Favored : 95.12 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.96 (0.17), residues: 2559 helix: 1.23 (0.15), residues: 1209 sheet: 0.99 (0.27), residues: 372 loop : -0.14 (0.21), residues: 978 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 221 time to evaluate : 2.449 Fit side-chains outliers start: 62 outliers final: 49 residues processed: 271 average time/residue: 1.5425 time to fit residues: 472.8147 Evaluate side-chains 265 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 42 residues processed: 9 average time/residue: 0.5256 time to fit residues: 9.9255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 23127 Z= 0.338 Angle : 0.594 7.492 31293 Z= 0.310 Chirality : 0.047 0.221 3207 Planarity : 0.005 0.046 3732 Dihedral : 13.246 121.210 3726 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.51 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.87 (0.17), residues: 2559 helix: 1.09 (0.15), residues: 1218 sheet: 0.94 (0.27), residues: 372 loop : -0.10 (0.20), residues: 969 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 216 time to evaluate : 2.787 Fit side-chains outliers start: 60 outliers final: 48 residues processed: 263 average time/residue: 1.6599 time to fit residues: 495.2922 Evaluate side-chains 261 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 2.647 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 41 residues processed: 9 average time/residue: 0.5795 time to fit residues: 10.4869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 0.4980 chunk 242 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 254 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23127 Z= 0.192 Angle : 0.548 7.370 31293 Z= 0.284 Chirality : 0.045 0.195 3207 Planarity : 0.004 0.043 3732 Dihedral : 12.875 115.580 3726 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.73 % Favored : 95.12 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.96 (0.17), residues: 2559 helix: 1.21 (0.15), residues: 1203 sheet: 0.99 (0.27), residues: 372 loop : -0.10 (0.21), residues: 984 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 2.681 Fit side-chains outliers start: 49 outliers final: 42 residues processed: 261 average time/residue: 1.6026 time to fit residues: 471.0198 Evaluate side-chains 255 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 2.350 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 41 residues processed: 3 average time/residue: 0.5760 time to fit residues: 5.4856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.077478 restraints weight = 28061.765| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.73 r_work: 0.2679 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1708 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 302, in __init__ self.caller(self.show_stats) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 337, in show_stats self.structure_monitor.show(prefix="",log=self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/__init__.py", line 150, in show self.update_statistics(prefix = prefix, log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/__init__.py", line 157, in update_statistics gs.show(prefix=prefix, log=log, uppercase=False) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/model/statistics.py", line 306, in show res = self.result() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/model/statistics.py", line 251, in result clash = self.clash(), File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/model/statistics.py", line 179, in clash nuclear = self.model.is_neutron()) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/validation/clashscore.py", line 139, in __init__ log=out) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/validation/clashscore.py", line 667, in check_and_add_hydrogen output_fname="reduce_fail.pdb") File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/validation/clashscore.py", line 568, in check_and_report_reduce_failure f.write(input_lines) IOError: [Errno 28] No space left on device