Starting phenix.real_space_refine (version: dev) on Tue Feb 21 06:09:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cal_30334/02_2023/7cal_30334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cal_30334/02_2023/7cal_30334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cal_30334/02_2023/7cal_30334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cal_30334/02_2023/7cal_30334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cal_30334/02_2023/7cal_30334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cal_30334/02_2023/7cal_30334_updated.pdb" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B ASP 331": "OD1" <-> "OD2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C ASP 331": "OD1" <-> "OD2" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "D TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "D ASP 331": "OD1" <-> "OD2" Residue "D TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 485": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14064 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3465 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3465 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3465 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "D" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3465 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.57, per 1000 atoms: 0.61 Number of scatterers: 14064 At special positions: 0 Unit cell: (112.554, 112.554, 115.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 4 15.00 O 2416 8.00 N 2288 7.00 C 9292 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 2.1 seconds 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 4 sheets defined 42.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 removed outlier: 3.502A pdb=" N VAL A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 68 " --> pdb=" O MET A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 82 No H-bonds generated for 'chain 'A' and resid 79 through 82' Processing helix chain 'A' and resid 94 through 110 removed outlier: 3.798A pdb=" N ASN A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 151 through 154 removed outlier: 3.762A pdb=" N LEU A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 162 through 165 No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.636A pdb=" N LEU A 170 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 174 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 176 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER A 180 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 182 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 185 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 213 removed outlier: 3.722A pdb=" N CYS A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.691A pdb=" N LEU A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.532A pdb=" N TYR A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 322 removed outlier: 3.652A pdb=" N ALA A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 removed outlier: 4.479A pdb=" N GLN A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.817A pdb=" N ASN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 483 through 490 removed outlier: 4.203A pdb=" N VAL A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 71 removed outlier: 3.501A pdb=" N VAL B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 68 " --> pdb=" O MET B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 94 through 110 removed outlier: 3.797A pdb=" N ASN B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'B' and resid 151 through 154 removed outlier: 3.762A pdb=" N LEU B 154 " --> pdb=" O LEU B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 162 through 165 No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 167 through 185 removed outlier: 3.636A pdb=" N LEU B 170 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 171 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 174 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 176 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 177 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 179 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER B 180 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 182 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 185 " --> pdb=" O PHE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 213 removed outlier: 3.723A pdb=" N CYS B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B 199 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 271 through 281 removed outlier: 3.692A pdb=" N LEU B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 302 removed outlier: 3.532A pdb=" N TYR B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.652A pdb=" N ALA B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 removed outlier: 4.478A pdb=" N GLN B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 removed outlier: 3.816A pdb=" N ASN B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 483 through 490 removed outlier: 4.202A pdb=" N VAL B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 71 removed outlier: 3.501A pdb=" N VAL C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 68 " --> pdb=" O MET C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 82 No H-bonds generated for 'chain 'C' and resid 79 through 82' Processing helix chain 'C' and resid 94 through 110 removed outlier: 3.797A pdb=" N ASN C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 105 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 136 Processing helix chain 'C' and resid 151 through 154 removed outlier: 3.762A pdb=" N LEU C 154 " --> pdb=" O LEU C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 162 through 165 No H-bonds generated for 'chain 'C' and resid 162 through 165' Processing helix chain 'C' and resid 167 through 185 removed outlier: 3.636A pdb=" N LEU C 170 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 171 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG C 176 " --> pdb=" O TRP C 173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER C 180 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C 185 " --> pdb=" O PHE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 213 removed outlier: 3.722A pdb=" N CYS C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C 199 " --> pdb=" O TRP C 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 221 No H-bonds generated for 'chain 'C' and resid 218 through 221' Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 271 through 281 removed outlier: 3.692A pdb=" N LEU C 275 " --> pdb=" O PRO C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 removed outlier: 3.532A pdb=" N TYR C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 322 removed outlier: 3.652A pdb=" N ALA C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 343 removed outlier: 4.478A pdb=" N GLN C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS C 336 " --> pdb=" O GLN C 332 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 337 " --> pdb=" O MET C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 removed outlier: 3.816A pdb=" N ASN C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 483 through 490 removed outlier: 4.202A pdb=" N VAL C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.502A pdb=" N VAL D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 68 " --> pdb=" O MET D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 82 No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'D' and resid 94 through 110 removed outlier: 3.797A pdb=" N ASN D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 136 Processing helix chain 'D' and resid 151 through 154 removed outlier: 3.761A pdb=" N LEU D 154 " --> pdb=" O LEU D 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 154' Processing helix chain 'D' and resid 162 through 165 No H-bonds generated for 'chain 'D' and resid 162 through 165' Processing helix chain 'D' and resid 167 through 185 removed outlier: 3.636A pdb=" N LEU D 170 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 171 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG D 174 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG D 176 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 179 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D 180 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA D 183 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 185 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 213 removed outlier: 3.722A pdb=" N CYS D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR D 199 " --> pdb=" O TRP D 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 221 No H-bonds generated for 'chain 'D' and resid 218 through 221' Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 271 through 281 removed outlier: 3.691A pdb=" N LEU D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 302 removed outlier: 3.531A pdb=" N TYR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 322 removed outlier: 3.652A pdb=" N ALA D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 343 removed outlier: 4.478A pdb=" N GLN D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 336 " --> pdb=" O GLN D 332 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 337 " --> pdb=" O MET D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 removed outlier: 3.817A pdb=" N ASN D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 483 through 490 removed outlier: 4.202A pdb=" N VAL D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 422 through 424 removed outlier: 3.992A pdb=" N VAL A 422 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 422 through 424 removed outlier: 3.993A pdb=" N VAL B 422 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 422 through 424 removed outlier: 3.993A pdb=" N VAL C 422 " --> pdb=" O PHE C 434 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 422 through 424 removed outlier: 3.993A pdb=" N VAL D 422 " --> pdb=" O PHE D 434 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1032 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: 3.28 Time building geometry restraints manager: 6.37 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: 2413 1.32 - 1.44: 4093 1.44 - 1.56: 7854 1.56 - 1.68: 0 1.68 - 1.80: 112 Bond restraints: 14472 Sorted by residual: bond pdb=" O13 3PE A 701 " pdb=" P 3PE A 701 " ideal model delta sigma weight residual 1.654 1.751 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" O13 3PE D 701 " pdb=" P 3PE D 701 " ideal model delta sigma weight residual 1.654 1.750 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O13 3PE C 701 " pdb=" P 3PE C 701 " ideal model delta sigma weight residual 1.654 1.750 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O13 3PE B 701 " pdb=" P 3PE B 701 " ideal model delta sigma weight residual 1.654 1.750 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O11 3PE A 701 " pdb=" P 3PE A 701 " ideal model delta sigma weight residual 1.644 1.696 -0.052 2.00e-02 2.50e+03 6.78e+00 ... (remaining 14467 not shown) Histogram of bond angle deviations from ideal: 90.34 - 99.44: 8 99.44 - 108.54: 951 108.54 - 117.65: 9181 117.65 - 126.75: 9303 126.75 - 135.86: 281 Bond angle restraints: 19724 Sorted by residual: angle pdb=" N VAL B 142 " pdb=" CA VAL B 142 " pdb=" C VAL B 142 " ideal model delta sigma weight residual 113.22 107.25 5.97 1.23e+00 6.61e-01 2.36e+01 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 113.22 107.30 5.92 1.23e+00 6.61e-01 2.32e+01 angle pdb=" N VAL C 142 " pdb=" CA VAL C 142 " pdb=" C VAL C 142 " ideal model delta sigma weight residual 113.22 107.30 5.92 1.23e+00 6.61e-01 2.31e+01 angle pdb=" N VAL A 142 " pdb=" CA VAL A 142 " pdb=" C VAL A 142 " ideal model delta sigma weight residual 113.22 107.31 5.91 1.23e+00 6.61e-01 2.31e+01 angle pdb=" C VAL C 426 " pdb=" N TYR C 427 " pdb=" CA TYR C 427 " ideal model delta sigma weight residual 120.38 126.93 -6.55 1.46e+00 4.69e-01 2.01e+01 ... (remaining 19719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 7203 15.26 - 30.52: 888 30.52 - 45.78: 203 45.78 - 61.04: 42 61.04 - 76.30: 8 Dihedral angle restraints: 8344 sinusoidal: 3088 harmonic: 5256 Sorted by residual: dihedral pdb=" CA MET C 476 " pdb=" C MET C 476 " pdb=" N SER C 477 " pdb=" CA SER C 477 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA MET D 476 " pdb=" C MET D 476 " pdb=" N SER D 477 " pdb=" CA SER D 477 " ideal model delta harmonic sigma weight residual 180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA MET A 476 " pdb=" C MET A 476 " pdb=" N SER A 477 " pdb=" CA SER A 477 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 8341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1424 0.053 - 0.106: 640 0.106 - 0.159: 122 0.159 - 0.213: 30 0.213 - 0.266: 8 Chirality restraints: 2224 Sorted by residual: chirality pdb=" CA TYR A 114 " pdb=" N TYR A 114 " pdb=" C TYR A 114 " pdb=" CB TYR A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TYR C 114 " pdb=" N TYR C 114 " pdb=" C TYR C 114 " pdb=" CB TYR C 114 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR B 114 " pdb=" N TYR B 114 " pdb=" C TYR B 114 " pdb=" CB TYR B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2221 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 77 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO A 78 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 77 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO D 78 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 78 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 78 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 77 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO C 78 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 78 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 78 " 0.033 5.00e-02 4.00e+02 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3961 2.79 - 3.32: 11862 3.32 - 3.85: 21646 3.85 - 4.37: 25945 4.37 - 4.90: 44332 Nonbonded interactions: 107746 Sorted by model distance: nonbonded pdb=" O TYR C 252 " pdb=" OG1 THR C 256 " model vdw 2.265 2.440 nonbonded pdb=" O TYR A 252 " pdb=" OG1 THR A 256 " model vdw 2.265 2.440 nonbonded pdb=" O TYR B 252 " pdb=" OG1 THR B 256 " model vdw 2.265 2.440 nonbonded pdb=" O TYR D 252 " pdb=" OG1 THR D 256 " model vdw 2.266 2.440 nonbonded pdb=" O SER A 152 " pdb=" OG SER A 152 " model vdw 2.348 2.440 ... (remaining 107741 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 64 5.16 5 C 9292 2.51 5 N 2288 2.21 5 O 2416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.200 Process input model: 37.150 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 0.097 14472 Z= 0.489 Angle : 1.092 12.067 19724 Z= 0.604 Chirality : 0.060 0.266 2224 Planarity : 0.007 0.057 2452 Dihedral : 14.516 76.300 4936 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.03 % Favored : 85.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.34 (0.13), residues: 1768 helix: -4.72 (0.06), residues: 928 sheet: None (None), residues: 0 loop : -3.52 (0.18), residues: 840 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.734 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2765 time to fit residues: 122.1204 Evaluate side-chains 250 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 301 HIS A 348 GLN A 365 ASN A 491 ASN B 294 ASN B 301 HIS B 365 ASN B 491 ASN C 294 ASN C 301 HIS C 365 ASN C 491 ASN D 294 ASN D 301 HIS D 365 ASN D 491 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14472 Z= 0.193 Angle : 0.652 5.949 19724 Z= 0.347 Chirality : 0.045 0.176 2224 Planarity : 0.005 0.050 2452 Dihedral : 8.572 59.892 2076 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.43 % Favored : 88.35 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.17), residues: 1768 helix: -2.89 (0.13), residues: 896 sheet: None (None), residues: 0 loop : -2.91 (0.20), residues: 872 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 275 time to evaluate : 1.653 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 28 residues processed: 294 average time/residue: 0.2614 time to fit residues: 111.3878 Evaluate side-chains 291 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 263 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1303 time to fit residues: 8.8716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 324 GLN A 407 GLN B 297 ASN B 407 GLN C 297 ASN C 407 GLN D 297 ASN D 407 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14472 Z= 0.242 Angle : 0.643 6.029 19724 Z= 0.336 Chirality : 0.046 0.177 2224 Planarity : 0.005 0.049 2452 Dihedral : 8.073 56.160 2076 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.88 % Favored : 87.90 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.19), residues: 1768 helix: -1.93 (0.16), residues: 920 sheet: None (None), residues: 0 loop : -2.67 (0.21), residues: 848 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 266 time to evaluate : 1.497 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 285 average time/residue: 0.2558 time to fit residues: 107.0302 Evaluate side-chains 271 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 260 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1232 time to fit residues: 4.7594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 170 optimal weight: 0.4980 chunk 152 optimal weight: 0.0060 chunk 45 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 374 ASN B 284 ASN B 374 ASN C 284 ASN C 297 ASN D 284 ASN D 297 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 14472 Z= 0.138 Angle : 0.555 6.481 19724 Z= 0.289 Chirality : 0.042 0.157 2224 Planarity : 0.004 0.048 2452 Dihedral : 7.306 53.968 2076 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.86 % Favored : 88.91 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.20), residues: 1768 helix: -1.41 (0.17), residues: 928 sheet: None (None), residues: 0 loop : -2.57 (0.21), residues: 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 296 time to evaluate : 1.685 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 301 average time/residue: 0.2596 time to fit residues: 113.6502 Evaluate side-chains 282 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 276 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1240 time to fit residues: 3.5886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 0.0870 chunk 152 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 374 ASN B 297 ASN B 374 ASN C 297 ASN C 374 ASN D 297 ASN D 374 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 14472 Z= 0.147 Angle : 0.557 6.801 19724 Z= 0.290 Chirality : 0.042 0.154 2224 Planarity : 0.004 0.045 2452 Dihedral : 6.941 56.948 2076 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.07 % Favored : 89.71 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.20), residues: 1768 helix: -0.97 (0.18), residues: 908 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 860 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 286 time to evaluate : 1.649 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 293 average time/residue: 0.2614 time to fit residues: 111.1143 Evaluate side-chains 269 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 263 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1223 time to fit residues: 3.6206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 170 optimal weight: 6.9990 chunk 141 optimal weight: 0.0170 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 0.5980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 354 ASN A 374 ASN B 99 ASN B 284 ASN B 297 ASN B 354 ASN B 374 ASN C 284 ASN C 297 ASN C 354 ASN C 374 ASN D 284 ASN D 297 ASN D 354 ASN D 374 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 14472 Z= 0.144 Angle : 0.571 9.523 19724 Z= 0.287 Chirality : 0.043 0.148 2224 Planarity : 0.004 0.045 2452 Dihedral : 6.708 58.537 2076 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.63 % Favored : 89.14 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.21), residues: 1768 helix: -0.88 (0.18), residues: 932 sheet: None (None), residues: 0 loop : -2.31 (0.22), residues: 836 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 279 time to evaluate : 1.724 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 296 average time/residue: 0.2634 time to fit residues: 113.8130 Evaluate side-chains 286 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 272 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1407 time to fit residues: 5.8191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 0.0170 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 354 ASN A 374 ASN B 99 ASN B 284 ASN B 354 ASN B 374 ASN C 99 ASN C 284 ASN C 297 ASN C 354 ASN C 374 ASN D 99 ASN D 284 ASN D 297 ASN D 354 ASN D 374 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14472 Z= 0.212 Angle : 0.625 10.452 19724 Z= 0.312 Chirality : 0.045 0.159 2224 Planarity : 0.004 0.046 2452 Dihedral : 7.031 59.413 2076 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.03 % Favored : 88.74 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.20), residues: 1768 helix: -0.90 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -2.34 (0.22), residues: 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 275 time to evaluate : 1.628 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 300 average time/residue: 0.2576 time to fit residues: 112.7480 Evaluate side-chains 288 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 272 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1244 time to fit residues: 5.9193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 154 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 284 ASN A 354 ASN A 374 ASN B 99 ASN B 354 ASN B 374 ASN C 99 ASN C 354 ASN C 374 ASN D 99 ASN D 354 ASN D 374 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 14472 Z= 0.152 Angle : 0.585 9.157 19724 Z= 0.292 Chirality : 0.043 0.231 2224 Planarity : 0.004 0.045 2452 Dihedral : 6.772 57.441 2076 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.69 % Favored : 89.08 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.21), residues: 1768 helix: -0.69 (0.18), residues: 968 sheet: None (None), residues: 0 loop : -2.28 (0.23), residues: 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 285 time to evaluate : 1.425 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 297 average time/residue: 0.2571 time to fit residues: 112.5633 Evaluate side-chains 287 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1255 time to fit residues: 3.7069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 95 optimal weight: 0.0060 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 354 ASN B 99 ASN B 354 ASN B 374 ASN C 354 ASN C 374 ASN D 354 ASN D 374 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 14472 Z= 0.149 Angle : 0.589 9.977 19724 Z= 0.289 Chirality : 0.043 0.216 2224 Planarity : 0.004 0.050 2452 Dihedral : 6.535 54.767 2076 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.12 % Favored : 89.65 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1768 helix: -0.44 (0.18), residues: 948 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 820 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 292 time to evaluate : 1.650 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 303 average time/residue: 0.2595 time to fit residues: 115.0546 Evaluate side-chains 286 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1225 time to fit residues: 2.4469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 354 ASN A 374 ASN B 99 ASN B 284 ASN B 354 ASN C 284 ASN C 354 ASN C 374 ASN D 284 ASN D 354 ASN D 374 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14472 Z= 0.163 Angle : 0.615 9.796 19724 Z= 0.296 Chirality : 0.043 0.283 2224 Planarity : 0.004 0.051 2452 Dihedral : 6.532 55.663 2076 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.18 % Favored : 89.59 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1768 helix: -0.35 (0.18), residues: 944 sheet: None (None), residues: 0 loop : -2.26 (0.23), residues: 824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 290 time to evaluate : 1.587 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 294 average time/residue: 0.2676 time to fit residues: 114.2715 Evaluate side-chains 283 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.3980 chunk 42 optimal weight: 0.0470 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 354 ASN B 99 ASN B 354 ASN B 374 ASN C 284 ASN C 354 ASN C 374 ASN D 284 ASN D 354 ASN D 374 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124776 restraints weight = 17720.178| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.85 r_work: 0.3256 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14472 Z= 0.203 Angle : 0.643 9.383 19724 Z= 0.313 Chirality : 0.045 0.295 2224 Planarity : 0.004 0.047 2452 Dihedral : 6.756 58.647 2076 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.75 % Favored : 89.03 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.21), residues: 1768 helix: -0.40 (0.18), residues: 948 sheet: None (None), residues: 0 loop : -2.25 (0.23), residues: 820 =============================================================================== Job complete usr+sys time: 3202.25 seconds wall clock time: 58 minutes 11.92 seconds (3491.92 seconds total)