Starting phenix.real_space_refine (version: dev) on Wed Feb 22 07:55:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/02_2023/5uvn_8608_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/02_2023/5uvn_8608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/02_2023/5uvn_8608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/02_2023/5uvn_8608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/02_2023/5uvn_8608_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/02_2023/5uvn_8608_neut.pdb" } resolution = 3.96 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= 0.001 sd= 0.010 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 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "F TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16902 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "C" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "D" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "E" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "F" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Time building chain proxies: 10.16, per 1000 atoms: 0.60 Number of scatterers: 16902 At special positions: 0 Unit cell: (106.11, 111.35, 168.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 3228 8.00 N 2886 7.00 C 10770 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: 7.37 Conformation dependent library (CDL) restraints added in 2.6 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 30 sheets defined 30.4% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU A 95 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 98 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 430 Processing helix chain 'A' and resid 436 through 467 Processing helix chain 'B' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU B 95 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 430 Processing helix chain 'B' and resid 436 through 467 Processing helix chain 'C' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU C 95 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 98 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 238 through 245 removed outlier: 4.035A pdb=" N THR C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 281 Processing helix chain 'C' and resid 322 through 333 removed outlier: 3.630A pdb=" N GLN C 327 " --> pdb=" O PRO C 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 346 Processing helix chain 'C' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 Processing helix chain 'C' and resid 436 through 467 Processing helix chain 'D' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU D 95 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 98 " --> pdb=" O GLU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 238 through 245 removed outlier: 4.035A pdb=" N THR D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'D' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN D 327 " --> pdb=" O PRO D 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 430 Processing helix chain 'D' and resid 436 through 467 Processing helix chain 'E' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU E 95 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 98 " --> pdb=" O GLU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 281 Processing helix chain 'E' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN E 327 " --> pdb=" O PRO E 323 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 430 Processing helix chain 'E' and resid 436 through 467 Processing helix chain 'F' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU F 95 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS F 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 98 " --> pdb=" O GLU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 244 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 281 Processing helix chain 'F' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN F 327 " --> pdb=" O PRO F 323 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 430 Processing helix chain 'F' and resid 436 through 467 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU A 85 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 75 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS A 87 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 62 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE A 104 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE A 178 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 186 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE A 203 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE A 268 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 161 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 236 Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU A 386 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 306 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 313 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 307 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE A 407 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 289 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1003 through 1006 Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 49 removed outlier: 6.839A pdb=" N GLU B 85 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 75 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS B 87 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 62 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE B 104 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE B 178 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 186 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 203 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE B 268 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 161 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 236 Processing sheet with id=AB2, first strand: chain 'B' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU B 386 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU B 306 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 313 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE B 307 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE B 407 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 289 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU C 85 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA C 75 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS C 87 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 62 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE C 104 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE C 178 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL C 186 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE C 203 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE C 268 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 161 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 236 Processing sheet with id=AB7, first strand: chain 'C' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU C 386 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU C 306 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 313 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE C 307 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE C 407 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 289 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU D 85 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA D 75 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS D 87 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 62 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE D 104 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE D 178 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL D 186 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE D 203 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE D 268 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE D 161 " --> pdb=" O PHE D 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 236 Processing sheet with id=AC3, first strand: chain 'D' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU D 386 " --> pdb=" O PRO D 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU D 306 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 313 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE D 307 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG D 311 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE D 407 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 289 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 44 through 49 removed outlier: 6.837A pdb=" N GLU E 85 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA E 75 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS E 87 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 62 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE E 104 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE E 178 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG E 182 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL E 186 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE E 203 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE E 268 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE E 161 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 234 through 236 Processing sheet with id=AC8, first strand: chain 'E' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU E 386 " --> pdb=" O PRO E 304 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU E 306 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 313 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE E 307 " --> pdb=" O ARG E 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG E 311 " --> pdb=" O PHE E 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE E 407 " --> pdb=" O ASP E 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU E 289 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 44 through 49 removed outlier: 6.839A pdb=" N GLU F 85 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA F 75 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS F 87 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE F 62 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE F 104 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 217 through 221 removed outlier: 6.371A pdb=" N PHE F 178 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG F 182 " --> pdb=" O PHE F 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL F 186 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE F 203 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE F 268 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 161 " --> pdb=" O PHE F 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU F 386 " --> pdb=" O PRO F 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU F 306 " --> pdb=" O LEU F 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY F 313 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE F 307 " --> pdb=" O ARG F 311 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE F 407 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU F 289 " --> pdb=" O ILE F 407 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2034 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: 5.35 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4940 1.33 - 1.45: 2492 1.45 - 1.57: 9704 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 17172 Sorted by residual: bond pdb=" C LEU F 299 " pdb=" N GLN F 300 " ideal model delta sigma weight residual 1.335 1.216 0.119 3.59e-02 7.76e+02 1.09e+01 bond pdb=" C LEU B 299 " pdb=" N GLN B 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.09e+01 bond pdb=" C LEU A 299 " pdb=" N GLN A 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.08e+01 bond pdb=" C LEU D 299 " pdb=" N GLN D 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.08e+01 bond pdb=" C LEU E 299 " pdb=" N GLN E 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.07e+01 ... (remaining 17167 not shown) Histogram of bond angle deviations from ideal: 96.30 - 104.27: 365 104.27 - 112.24: 9447 112.24 - 120.21: 6236 120.21 - 128.18: 7383 128.18 - 136.16: 101 Bond angle restraints: 23532 Sorted by residual: angle pdb=" C SER B 239 " pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 117.23 109.03 8.20 1.36e+00 5.41e-01 3.64e+01 angle pdb=" C SER E 239 " pdb=" CA SER E 239 " pdb=" CB SER E 239 " ideal model delta sigma weight residual 117.23 109.04 8.19 1.36e+00 5.41e-01 3.62e+01 angle pdb=" C SER A 239 " pdb=" CA SER A 239 " pdb=" CB SER A 239 " ideal model delta sigma weight residual 117.23 109.06 8.17 1.36e+00 5.41e-01 3.61e+01 angle pdb=" C SER D 239 " pdb=" CA SER D 239 " pdb=" CB SER D 239 " ideal model delta sigma weight residual 117.23 109.06 8.17 1.36e+00 5.41e-01 3.61e+01 angle pdb=" C SER F 239 " pdb=" CA SER F 239 " pdb=" CB SER F 239 " ideal model delta sigma weight residual 117.23 109.08 8.15 1.36e+00 5.41e-01 3.60e+01 ... (remaining 23527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.39: 8351 7.39 - 14.79: 1382 14.79 - 22.18: 293 22.18 - 29.58: 60 29.58 - 36.97: 6 Dihedral angle restraints: 10092 sinusoidal: 3018 harmonic: 7074 Sorted by residual: dihedral pdb=" CA ASP E 294 " pdb=" C ASP E 294 " pdb=" N SER E 295 " pdb=" CA SER E 295 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASP D 294 " pdb=" C ASP D 294 " pdb=" N SER D 295 " pdb=" CA SER D 295 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N SER A 295 " pdb=" CA SER A 295 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 10089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1891 0.052 - 0.104: 846 0.104 - 0.155: 180 0.155 - 0.207: 20 0.207 - 0.259: 9 Chirality restraints: 2946 Sorted by residual: chirality pdb=" CG LEU D 170 " pdb=" CB LEU D 170 " pdb=" CD1 LEU D 170 " pdb=" CD2 LEU D 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU F 170 " pdb=" CB LEU F 170 " pdb=" CD1 LEU F 170 " pdb=" CD2 LEU F 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2943 not shown) Planarity restraints: 3054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK C 456 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C UNK C 456 " -0.064 2.00e-02 2.50e+03 pdb=" O UNK C 456 " 0.024 2.00e-02 2.50e+03 pdb=" N UNK C 457 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK E 456 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C UNK E 456 " -0.063 2.00e-02 2.50e+03 pdb=" O UNK E 456 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK E 457 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK D 456 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C UNK D 456 " -0.063 2.00e-02 2.50e+03 pdb=" O UNK D 456 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK D 457 " 0.021 2.00e-02 2.50e+03 ... (remaining 3051 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 244 2.59 - 3.17: 16152 3.17 - 3.75: 23691 3.75 - 4.32: 32837 4.32 - 4.90: 53502 Nonbonded interactions: 126426 Sorted by model distance: nonbonded pdb=" NH1 ARG A 65 " pdb=" O LEU F 81 " model vdw 2.013 2.520 nonbonded pdb=" O LEU D 81 " pdb=" NH1 ARG E 65 " model vdw 2.016 2.520 nonbonded pdb=" O LEU A 81 " pdb=" NH1 ARG B 65 " model vdw 2.017 2.520 nonbonded pdb=" O LEU C 81 " pdb=" NH1 ARG D 65 " model vdw 2.023 2.520 nonbonded pdb=" O LEU B 81 " pdb=" NH1 ARG C 65 " model vdw 2.024 2.520 ... (remaining 126421 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' selection = chain 'E' selection = chain 'F' } 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 10770 2.51 5 N 2886 2.21 5 O 3228 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 group one per residue 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: 0.450 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: 3.430 Check model and map are aligned: 0.260 Process input model: 45.280 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 : 0.012 0.119 17172 Z= 0.798 Angle : 1.132 9.262 23532 Z= 0.594 Chirality : 0.059 0.259 2946 Planarity : 0.008 0.078 3054 Dihedral : 7.901 36.971 5544 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.54 % Favored : 90.91 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -4.03 (0.14), residues: 2178 helix: -3.73 (0.20), residues: 354 sheet: -2.16 (0.14), residues: 612 loop : -2.64 (0.14), residues: 1212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 422 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 422 average time/residue: 0.2921 time to fit residues: 181.5910 Evaluate side-chains 244 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 143 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 215 ASN A 285 HIS A 359 HIS A 376 ASN B 215 ASN B 285 HIS B 359 HIS B 376 ASN C 201 GLN C 215 ASN C 285 HIS C 359 HIS C 376 ASN D 201 GLN D 215 ASN D 285 HIS D 359 HIS D 376 ASN E 201 GLN E 215 ASN E 285 HIS E 359 HIS E 376 ASN F 201 GLN F 215 ASN F 285 HIS F 359 HIS F 376 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 17172 Z= 0.212 Angle : 0.719 8.161 23532 Z= 0.369 Chirality : 0.047 0.151 2946 Planarity : 0.006 0.062 3054 Dihedral : 6.441 23.319 2592 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.54 % Favored : 90.63 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.07 (0.16), residues: 2178 helix: -2.79 (0.20), residues: 396 sheet: -1.49 (0.15), residues: 726 loop : -2.04 (0.18), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 356 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 372 average time/residue: 0.2758 time to fit residues: 154.6044 Evaluate side-chains 275 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 257 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1471 time to fit residues: 7.6219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 185 optimal weight: 0.0270 chunk 152 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 223 optimal weight: 0.8980 chunk 241 optimal weight: 30.0000 chunk 199 optimal weight: 30.0000 chunk 221 optimal weight: 0.8980 chunk 76 optimal weight: 30.0000 chunk 179 optimal weight: 6.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN E 201 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 17172 Z= 0.179 Angle : 0.668 13.321 23532 Z= 0.337 Chirality : 0.046 0.140 2946 Planarity : 0.005 0.061 3054 Dihedral : 5.606 23.327 2592 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.85 % Favored : 91.32 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.22 (0.16), residues: 2178 helix: -1.08 (0.25), residues: 360 sheet: -0.97 (0.16), residues: 720 loop : -1.93 (0.18), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 330 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 356 average time/residue: 0.2730 time to fit residues: 149.4142 Evaluate side-chains 289 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1525 time to fit residues: 6.7097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 224 optimal weight: 0.0270 chunk 237 optimal weight: 6.9990 chunk 117 optimal weight: 30.0000 chunk 212 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 17172 Z= 0.407 Angle : 0.776 11.375 23532 Z= 0.387 Chirality : 0.049 0.170 2946 Planarity : 0.006 0.066 3054 Dihedral : 5.831 23.295 2592 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 1.10 % Allowed : 8.63 % Favored : 90.27 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.40 (0.16), residues: 2178 helix: -0.62 (0.26), residues: 360 sheet: -1.04 (0.16), residues: 714 loop : -2.32 (0.17), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 267 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 26 residues processed: 299 average time/residue: 0.2653 time to fit residues: 121.7086 Evaluate side-chains 284 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 258 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1424 time to fit residues: 9.4386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 202 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 17172 Z= 0.286 Angle : 0.697 13.224 23532 Z= 0.350 Chirality : 0.047 0.139 2946 Planarity : 0.005 0.065 3054 Dihedral : 5.528 24.127 2592 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.23 % Favored : 89.94 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.16 (0.17), residues: 2178 helix: -0.05 (0.28), residues: 360 sheet: -0.97 (0.17), residues: 714 loop : -2.26 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 276 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 295 average time/residue: 0.2811 time to fit residues: 126.0756 Evaluate side-chains 270 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 255 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1933 time to fit residues: 7.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17172 Z= 0.245 Angle : 0.677 13.848 23532 Z= 0.340 Chirality : 0.046 0.141 2946 Planarity : 0.005 0.063 3054 Dihedral : 5.260 24.109 2592 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.87 % Favored : 89.30 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.89 (0.17), residues: 2178 helix: 0.34 (0.29), residues: 360 sheet: -0.83 (0.17), residues: 714 loop : -2.13 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 311 average time/residue: 0.2826 time to fit residues: 133.7253 Evaluate side-chains 271 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 257 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1459 time to fit residues: 6.2206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 132 optimal weight: 0.5980 chunk 237 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 17172 Z= 0.316 Angle : 0.729 16.088 23532 Z= 0.363 Chirality : 0.048 0.142 2946 Planarity : 0.005 0.065 3054 Dihedral : 5.369 23.870 2592 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.19 % Favored : 88.98 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.89 (0.17), residues: 2178 helix: 0.45 (0.29), residues: 360 sheet: -0.85 (0.17), residues: 714 loop : -2.16 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 280 average time/residue: 0.2751 time to fit residues: 117.7849 Evaluate side-chains 265 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 251 time to evaluate : 2.063 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1729 time to fit residues: 6.9799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 17172 Z= 0.268 Angle : 0.707 17.749 23532 Z= 0.353 Chirality : 0.047 0.142 2946 Planarity : 0.005 0.064 3054 Dihedral : 5.193 24.302 2592 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.01 % Favored : 89.16 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.75 (0.18), residues: 2178 helix: 0.63 (0.30), residues: 360 sheet: -0.76 (0.17), residues: 714 loop : -2.09 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 273 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 287 average time/residue: 0.2730 time to fit residues: 120.8104 Evaluate side-chains 274 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 266 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2792 time to fit residues: 5.8272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 0.0980 chunk 227 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 199 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 145 optimal weight: 0.0030 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17172 Z= 0.183 Angle : 0.672 16.117 23532 Z= 0.337 Chirality : 0.046 0.158 2946 Planarity : 0.005 0.061 3054 Dihedral : 4.849 23.737 2592 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.23 % Favored : 89.85 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.46 (0.18), residues: 2178 helix: 0.88 (0.30), residues: 360 sheet: -0.59 (0.18), residues: 726 loop : -1.91 (0.19), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 303 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 307 average time/residue: 0.2850 time to fit residues: 132.5304 Evaluate side-chains 277 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.931 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 110 optimal weight: 0.0570 chunk 162 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 225 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 119 optimal weight: 30.0000 chunk 155 optimal weight: 0.8980 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17172 Z= 0.216 Angle : 0.709 15.890 23532 Z= 0.350 Chirality : 0.046 0.198 2946 Planarity : 0.005 0.063 3054 Dihedral : 4.876 23.282 2592 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.83 % Favored : 89.53 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.51 (0.18), residues: 2178 helix: 0.87 (0.30), residues: 360 sheet: -0.71 (0.17), residues: 774 loop : -1.91 (0.20), residues: 1044 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 276 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 284 average time/residue: 0.2834 time to fit residues: 123.2712 Evaluate side-chains 268 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 263 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2769 time to fit residues: 4.7019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098523 restraints weight = 30653.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100370 restraints weight = 22457.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101488 restraints weight = 18019.519| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 17172 Z= 0.430 Angle : 0.827 16.252 23532 Z= 0.409 Chirality : 0.050 0.262 2946 Planarity : 0.006 0.067 3054 Dihedral : 5.469 22.690 2592 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.33 % Favored : 88.93 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.96 (0.18), residues: 2178 helix: 0.39 (0.29), residues: 360 sheet: -1.04 (0.17), residues: 774 loop : -2.11 (0.19), residues: 1044 =============================================================================== Job complete usr+sys time: 3089.11 seconds wall clock time: 56 minutes 30.82 seconds (3390.82 seconds total)