Starting phenix.real_space_refine (version: dev) on Wed Dec 14 00:24:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/12_2022/8f0a_28754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/12_2022/8f0a_28754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/12_2022/8f0a_28754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/12_2022/8f0a_28754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/12_2022/8f0a_28754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/12_2022/8f0a_28754.pdb" } resolution = 2.6 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= 0.053 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18060 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "B" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "C" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "D" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "E" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "a" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "b" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "c" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 8.21, per 1000 atoms: 0.45 Number of scatterers: 18060 At special positions: 0 Unit cell: (98.58, 112.36, 126.14, 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 42 16.00 O 1716 8.00 N 1566 7.00 C 5547 6.00 H 9189 1.00 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: 15.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 21 sheets defined 23.3% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 24 Proline residue: A 24 - end of helix No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.610A pdb=" N GLN A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 21 through 24 Proline residue: B 24 - end of helix No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 21 through 24 Proline residue: C 24 - end of helix No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 280 Processing helix chain 'C' and resid 297 through 303 Processing helix chain 'C' and resid 320 through 329 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 417 through 426 Processing helix chain 'F' and resid 394 through 399 Processing helix chain 'F' and resid 417 through 426 Processing helix chain 'a' and resid 37 through 49 Processing helix chain 'b' and resid 37 through 49 Processing helix chain 'c' and resid 37 through 49 Processing sheet with id=AA1, first strand: chain 'a' and resid 34 through 36 removed outlier: 4.250A pdb=" N MET A 85 " --> pdb=" O PHE a 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER A 89 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN A 103 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 99 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 136 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 130 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 138 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 113 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET A 127 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR A 111 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU A 32 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 113 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 30 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL A 115 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER A 28 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN A 225 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 242 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 200 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU A 185 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 214 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 317 removed outlier: 6.565A pdb=" N GLY A 340 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 338 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 316 through 317 removed outlier: 6.661A pdb=" N MET A 268 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 34 through 36 removed outlier: 4.253A pdb=" N MET B 85 " --> pdb=" O PHE b 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 89 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 103 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR B 99 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 136 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS B 130 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 138 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 113 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET B 127 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N THR B 111 " --> pdb=" O MET B 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU B 32 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE B 113 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 30 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 115 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 28 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 29 through 31 removed outlier: 5.793A pdb=" N ASN B 225 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE B 242 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN B 200 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU B 185 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 214 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AA9, first strand: chain 'B' and resid 316 through 317 removed outlier: 6.565A pdb=" N GLY B 340 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU B 313 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR B 338 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 316 through 317 removed outlier: 6.662A pdb=" N MET B 268 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET C 85 " --> pdb=" O PHE c 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER C 89 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN C 103 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR C 99 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 136 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS C 130 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 138 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C 113 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET C 127 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N THR C 111 " --> pdb=" O MET C 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU C 32 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE C 113 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN C 30 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 115 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER C 28 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN C 225 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 242 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN C 200 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU C 185 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 214 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AB5, first strand: chain 'C' and resid 316 through 317 removed outlier: 6.566A pdb=" N GLY C 340 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 313 " --> pdb=" O THR C 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 338 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 316 through 317 removed outlier: 6.663A pdb=" N MET C 268 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN D 435 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA D 410 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA D 433 " --> pdb=" O ALA D 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 375 through 378 removed outlier: 6.506A pdb=" N GLU E 375 " --> pdb=" O ASN E 388 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 375 through 378 removed outlier: 6.506A pdb=" N GLU E 375 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN E 435 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA E 410 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA E 433 " --> pdb=" O ALA E 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 375 through 378 removed outlier: 6.505A pdb=" N GLU F 375 " --> pdb=" O ASN F 388 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 375 through 378 removed outlier: 6.505A pdb=" N GLU F 375 " --> pdb=" O ASN F 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN F 435 " --> pdb=" O ILE F 408 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA F 410 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA F 433 " --> pdb=" O ALA F 410 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1062 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: 8.12 Time building geometry restraints manager: 16.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 9189 1.13 - 1.30: 1766 1.30 - 1.48: 3762 1.48 - 1.65: 3340 1.65 - 1.83: 84 Bond restraints: 18141 Sorted by residual: bond pdb=" CB HIS a 33 " pdb=" CG HIS a 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" CB HIS b 33 " pdb=" CG HIS b 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CB HIS c 33 " pdb=" CG HIS c 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CB LEU b 32 " pdb=" CG LEU b 32 " ideal model delta sigma weight residual 1.530 1.327 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" CB LEU c 32 " pdb=" CG LEU c 32 " ideal model delta sigma weight residual 1.530 1.328 0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 18136 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.94: 503 105.94 - 113.00: 21591 113.00 - 120.07: 5935 120.07 - 127.14: 4886 127.14 - 134.21: 49 Bond angle restraints: 32964 Sorted by residual: angle pdb=" C ASP A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.02e+00 9.61e-01 6.37e+01 angle pdb=" C ASP B 131 " pdb=" N PRO B 132 " pdb=" CA PRO B 132 " ideal model delta sigma weight residual 119.56 127.65 -8.09 1.02e+00 9.61e-01 6.29e+01 angle pdb=" N LEU b 32 " pdb=" CA LEU b 32 " pdb=" C LEU b 32 " ideal model delta sigma weight residual 110.68 121.67 -10.99 1.39e+00 5.18e-01 6.25e+01 angle pdb=" N LEU a 32 " pdb=" CA LEU a 32 " pdb=" C LEU a 32 " ideal model delta sigma weight residual 110.68 121.66 -10.98 1.39e+00 5.18e-01 6.24e+01 angle pdb=" C ASP C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 119.56 127.61 -8.05 1.02e+00 9.61e-01 6.22e+01 ... (remaining 32959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 6795 16.51 - 33.03: 144 33.03 - 49.54: 45 49.54 - 66.05: 18 66.05 - 82.57: 9 Dihedral angle restraints: 7011 sinusoidal: 3387 harmonic: 3624 Sorted by residual: dihedral pdb=" CD2 HIS B 105 " pdb=" CG HIS B 105 " pdb=" ND1 HIS B 105 " pdb=" HD1 HIS B 105 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CD2 HIS C 105 " pdb=" CG HIS C 105 " pdb=" ND1 HIS C 105 " pdb=" HD1 HIS C 105 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CD2 HIS A 105 " pdb=" CG HIS A 105 " pdb=" ND1 HIS A 105 " pdb=" HD1 HIS A 105 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 7008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 858 0.110 - 0.219: 457 0.219 - 0.328: 111 0.328 - 0.438: 14 0.438 - 0.547: 9 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CG LEU C 87 " pdb=" CB LEU C 87 " pdb=" CD1 LEU C 87 " pdb=" CD2 LEU C 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" CG LEU A 87 " pdb=" CB LEU A 87 " pdb=" CD1 LEU A 87 " pdb=" CD2 LEU A 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.48e+00 chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 1446 not shown) Planarity restraints: 2739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 105 " 0.076 2.00e-02 2.50e+03 7.53e-02 1.28e+02 pdb=" CG HIS B 105 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS B 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS B 105 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS B 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS B 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS B 105 " -0.173 2.00e-02 2.50e+03 pdb=" HD2 HIS B 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS B 105 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 105 " -0.076 2.00e-02 2.50e+03 7.52e-02 1.27e+02 pdb=" CG HIS C 105 " -0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS C 105 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS C 105 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS C 105 " -0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS C 105 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS C 105 " 0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS C 105 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS C 105 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 105 " 0.076 2.00e-02 2.50e+03 7.50e-02 1.26e+02 pdb=" CG HIS A 105 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS A 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS A 105 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS A 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS A 105 " -0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS A 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS A 105 " 0.057 2.00e-02 2.50e+03 ... (remaining 2736 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 418 2.00 - 2.65: 24724 2.65 - 3.30: 52799 3.30 - 3.95: 71192 3.95 - 4.60: 110521 Nonbonded interactions: 259654 Sorted by model distance: nonbonded pdb=" H SER B 134 " pdb=" H ASP B 135 " model vdw 1.353 2.100 nonbonded pdb=" H SER A 134 " pdb=" H ASP A 135 " model vdw 1.355 2.100 nonbonded pdb=" H SER C 134 " pdb=" H ASP C 135 " model vdw 1.355 2.100 nonbonded pdb=" HZ3 LYS B 114 " pdb=" OD1 ASP B 124 " model vdw 1.618 1.850 nonbonded pdb=" HZ3 LYS A 114 " pdb=" OD1 ASP A 124 " model vdw 1.618 1.850 ... (remaining 259649 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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 S 42 5.16 5 C 5547 2.51 5 N 1566 2.21 5 O 1716 1.98 5 H 9189 0.53 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: 1.370 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: 0.390 Extract box with map and model: 5.650 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.170 Process input model: 61.010 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 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 : 0.031 0.203 8952 Z= 2.053 Angle : 1.768 10.986 12084 Z= 1.183 Chirality : 0.132 0.547 1449 Planarity : 0.010 0.075 1578 Dihedral : 9.862 82.565 3327 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.24), residues: 1188 helix: -0.93 (0.30), residues: 231 sheet: 1.04 (0.28), residues: 366 loop : 0.92 (0.24), residues: 591 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 255 average time/residue: 2.4780 time to fit residues: 675.3186 Evaluate side-chains 203 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2799 time to fit residues: 2.6626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.6637 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 8952 Z= 0.235 Angle : 0.703 6.336 12084 Z= 0.386 Chirality : 0.049 0.184 1449 Planarity : 0.004 0.039 1578 Dihedral : 7.435 86.465 1260 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.24), residues: 1188 helix: 1.10 (0.37), residues: 228 sheet: 0.83 (0.26), residues: 369 loop : 0.72 (0.24), residues: 591 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 230 average time/residue: 2.3819 time to fit residues: 587.0139 Evaluate side-chains 221 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 9 average time/residue: 0.3450 time to fit residues: 6.6723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 8952 Z= 0.345 Angle : 0.623 6.300 12084 Z= 0.339 Chirality : 0.047 0.161 1449 Planarity : 0.005 0.067 1578 Dihedral : 7.130 85.960 1260 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.24), residues: 1188 helix: 1.70 (0.38), residues: 228 sheet: 0.48 (0.27), residues: 354 loop : 0.53 (0.23), residues: 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 209 average time/residue: 2.4445 time to fit residues: 546.5666 Evaluate side-chains 203 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.5549 time to fit residues: 8.9076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 8952 Z= 0.383 Angle : 0.621 8.736 12084 Z= 0.331 Chirality : 0.047 0.151 1449 Planarity : 0.005 0.079 1578 Dihedral : 7.127 86.304 1260 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.24), residues: 1188 helix: 1.81 (0.37), residues: 225 sheet: 0.28 (0.26), residues: 384 loop : 0.41 (0.24), residues: 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 12 residues processed: 200 average time/residue: 2.3680 time to fit residues: 509.4398 Evaluate side-chains 203 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.7174 time to fit residues: 12.4116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8952 Z= 0.186 Angle : 0.582 7.799 12084 Z= 0.303 Chirality : 0.046 0.153 1449 Planarity : 0.004 0.061 1578 Dihedral : 7.067 86.130 1260 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.24), residues: 1188 helix: 1.97 (0.38), residues: 225 sheet: 0.29 (0.26), residues: 384 loop : 0.49 (0.25), residues: 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 198 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 198 average time/residue: 2.4063 time to fit residues: 512.9835 Evaluate side-chains 192 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.8950 time to fit residues: 3.7998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 7.9990 chunk 22 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 59 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8952 Z= 0.155 Angle : 0.567 8.271 12084 Z= 0.292 Chirality : 0.046 0.150 1449 Planarity : 0.004 0.056 1578 Dihedral : 6.986 85.736 1260 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.24), residues: 1188 helix: 2.06 (0.37), residues: 225 sheet: 0.36 (0.26), residues: 384 loop : 0.59 (0.25), residues: 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 201 average time/residue: 2.3627 time to fit residues: 509.4138 Evaluate side-chains 195 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.4880 time to fit residues: 5.0058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 95 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8952 Z= 0.156 Angle : 0.571 9.182 12084 Z= 0.291 Chirality : 0.046 0.146 1449 Planarity : 0.003 0.058 1578 Dihedral : 6.917 85.251 1260 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.24), residues: 1188 helix: 2.08 (0.37), residues: 225 sheet: 0.66 (0.26), residues: 363 loop : 0.56 (0.25), residues: 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 195 average time/residue: 2.6393 time to fit residues: 551.7354 Evaluate side-chains 195 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 4 average time/residue: 1.4563 time to fit residues: 9.9956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 102 optimal weight: 0.0970 chunk 108 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8952 Z= 0.195 Angle : 0.595 10.714 12084 Z= 0.299 Chirality : 0.046 0.192 1449 Planarity : 0.003 0.062 1578 Dihedral : 6.899 84.659 1260 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.24), residues: 1188 helix: 2.18 (0.37), residues: 225 sheet: 0.64 (0.28), residues: 339 loop : 0.52 (0.24), residues: 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 198 average time/residue: 2.3127 time to fit residues: 495.2196 Evaluate side-chains 196 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.8522 time to fit residues: 4.9297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8952 Z= 0.262 Angle : 0.624 12.162 12084 Z= 0.314 Chirality : 0.046 0.214 1449 Planarity : 0.004 0.064 1578 Dihedral : 6.907 83.997 1260 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.12 (0.24), residues: 1188 helix: 2.11 (0.37), residues: 228 sheet: 0.61 (0.27), residues: 342 loop : 0.42 (0.24), residues: 618 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 191 average time/residue: 2.4496 time to fit residues: 501.5224 Evaluate side-chains 184 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.1576 time to fit residues: 4.4449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 0.0000 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8952 Z= 0.160 Angle : 0.612 12.036 12084 Z= 0.304 Chirality : 0.046 0.162 1449 Planarity : 0.004 0.064 1578 Dihedral : 6.823 82.941 1260 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.24), residues: 1188 helix: 2.26 (0.37), residues: 228 sheet: 0.84 (0.28), residues: 336 loop : 0.45 (0.24), residues: 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 192 average time/residue: 2.4212 time to fit residues: 498.3286 Evaluate side-chains 183 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.8168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 38 optimal weight: 0.0050 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.052959 restraints weight = 56302.791| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.36 r_work: 0.2498 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8952 Z= 0.168 Angle : 0.614 11.997 12084 Z= 0.305 Chirality : 0.046 0.230 1449 Planarity : 0.004 0.068 1578 Dihedral : 6.790 84.196 1260 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.24), residues: 1188 helix: 2.27 (0.37), residues: 228 sheet: 0.91 (0.28), residues: 336 loop : 0.50 (0.24), residues: 624 =============================================================================== Job complete usr+sys time: 8692.71 seconds wall clock time: 152 minutes 13.49 seconds (9133.49 seconds total)