Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 03:16:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/10_2023/8f0a_28754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/10_2023/8f0a_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_28754/10_2023/8f0a_28754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/10_2023/8f0a_28754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/10_2023/8f0a_28754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0a_28754/10_2023/8f0a_28754.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 7.82, per 1000 atoms: 0.43 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: 15.91 Conformation dependent library (CDL) restraints added in 1.9 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: 1.58 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: 7.32 Time building geometry restraints manager: 16.09 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.260 Extract box with map and model: 4.350 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 61.010 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 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 % Allowed : 0.32 % Favored : 99.68 % 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 : 1.609 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: 3.0116 time to fit residues: 815.3653 Evaluate side-chains 203 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2904 time to fit residues: 2.5313 ------------------------------------------------------------------------------- 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: 0.6753 moved from start: 0.3101 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= 0.237 Angle : 0.702 6.401 12084 Z= 0.385 Chirality : 0.049 0.184 1449 Planarity : 0.004 0.039 1578 Dihedral : 7.430 86.462 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 % Allowed : 12.21 % Favored : 85.03 % 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: 0.84 (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 251 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 1.376 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: 229 average time/residue: 2.8160 time to fit residues: 685.7921 Evaluate side-chains 220 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 210 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 9 average time/residue: 0.2899 time to fit residues: 5.8444 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.0970 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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: 0.6817 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8952 Z= 0.282 Angle : 0.605 6.270 12084 Z= 0.328 Chirality : 0.046 0.159 1449 Planarity : 0.005 0.070 1578 Dihedral : 7.091 85.632 1260 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.12 % Allowed : 13.59 % Favored : 84.29 % 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: 1.04 (0.24), residues: 1188 helix: 1.75 (0.38), residues: 228 sheet: 0.41 (0.26), residues: 384 loop : 0.62 (0.24), residues: 576 *********************** 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 229 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 1.654 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 outliers start: 20 outliers final: 9 residues processed: 211 average time/residue: 2.8073 time to fit residues: 629.9260 Evaluate side-chains 213 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.6668 time to fit residues: 9.4181 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.6859 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 8952 Z= 0.390 Angle : 0.613 8.253 12084 Z= 0.327 Chirality : 0.047 0.154 1449 Planarity : 0.004 0.075 1578 Dihedral : 7.090 85.911 1260 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.23 % Allowed : 14.65 % Favored : 83.12 % 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: 0.88 (0.24), residues: 1188 helix: 1.84 (0.37), residues: 225 sheet: 0.30 (0.26), residues: 384 loop : 0.44 (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 219 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.757 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 outliers start: 21 outliers final: 12 residues processed: 199 average time/residue: 2.7802 time to fit residues: 588.7538 Evaluate side-chains 205 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 1.513 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5820 time to fit residues: 10.7136 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.6845 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8952 Z= 0.207 Angle : 0.584 8.897 12084 Z= 0.305 Chirality : 0.046 0.155 1449 Planarity : 0.004 0.052 1578 Dihedral : 7.068 85.743 1260 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.38 % Allowed : 16.03 % Favored : 82.59 % 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: 0.92 (0.24), residues: 1188 helix: 1.93 (0.37), residues: 228 sheet: 0.32 (0.26), residues: 384 loop : 0.43 (0.24), residues: 576 *********************** 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 211 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 1.491 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 outliers start: 13 outliers final: 7 residues processed: 199 average time/residue: 2.8403 time to fit residues: 601.1330 Evaluate side-chains 200 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 6 average time/residue: 0.9671 time to fit residues: 8.7601 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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: 0.6842 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8952 Z= 0.171 Angle : 0.572 7.528 12084 Z= 0.298 Chirality : 0.046 0.151 1449 Planarity : 0.003 0.054 1578 Dihedral : 6.994 85.380 1260 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.17 % Allowed : 17.09 % Favored : 81.74 % 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: 0.99 (0.24), residues: 1188 helix: 1.95 (0.37), residues: 228 sheet: 0.49 (0.26), residues: 369 loop : 0.38 (0.24), residues: 591 *********************** 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 208 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 1.636 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 outliers start: 11 outliers final: 6 residues processed: 199 average time/residue: 2.7778 time to fit residues: 588.2739 Evaluate side-chains 193 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 5 average time/residue: 0.4846 time to fit residues: 5.1303 ------------------------------------------------------------------------------- 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: 3.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.6850 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8952 Z= 0.180 Angle : 0.584 10.058 12084 Z= 0.297 Chirality : 0.045 0.147 1449 Planarity : 0.004 0.062 1578 Dihedral : 6.945 84.898 1260 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.85 % Allowed : 18.05 % Favored : 81.10 % 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: 1.07 (0.24), residues: 1188 helix: 2.04 (0.37), residues: 228 sheet: 0.51 (0.26), residues: 369 loop : 0.45 (0.25), residues: 591 *********************** 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 199 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.529 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: 8 outliers final: 8 residues processed: 192 average time/residue: 2.8374 time to fit residues: 579.5987 Evaluate side-chains 200 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 7 average time/residue: 0.6736 time to fit residues: 7.9084 ------------------------------------------------------------------------------- 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: 0.1980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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: 0.6854 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 0.039 8952 Z= 0.180 Angle : 0.588 12.189 12084 Z= 0.297 Chirality : 0.045 0.155 1449 Planarity : 0.004 0.063 1578 Dihedral : 6.923 84.202 1260 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.85 % Allowed : 18.37 % Favored : 80.79 % 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: 2.17 (0.37), residues: 228 sheet: 0.72 (0.28), residues: 333 loop : 0.47 (0.24), residues: 627 *********************** 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 : 1.525 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: 2 residues processed: 196 average time/residue: 2.7962 time to fit residues: 583.5319 Evaluate side-chains 189 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2401 time to fit residues: 2.7579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4517 > 50: distance: 103 - 134: 4.049 distance: 106 - 131: 3.439 distance: 123 - 131: 3.525 distance: 133 - 148: 4.055 distance: 137 - 139: 4.284 distance: 148 - 149: 5.142 distance: 148 - 153: 7.933 distance: 149 - 150: 4.897 distance: 149 - 152: 4.703 distance: 149 - 154: 5.336 distance: 150 - 151: 12.675 distance: 150 - 158: 5.759 distance: 152 - 156: 9.569 distance: 152 - 157: 9.203 distance: 158 - 159: 9.843 distance: 158 - 165: 4.618 distance: 159 - 160: 9.794 distance: 159 - 162: 8.487 distance: 159 - 166: 4.068 distance: 160 - 161: 17.489 distance: 160 - 174: 11.264 distance: 162 - 163: 7.004 distance: 162 - 164: 5.158 distance: 163 - 168: 7.001 distance: 163 - 169: 8.787 distance: 163 - 170: 9.554 distance: 164 - 171: 8.660 distance: 164 - 172: 8.094 distance: 164 - 173: 12.378 distance: 174 - 175: 9.664 distance: 174 - 183: 24.914 distance: 175 - 176: 7.868 distance: 175 - 178: 4.968 distance: 175 - 184: 8.092 distance: 176 - 177: 10.437 distance: 178 - 179: 3.894 distance: 178 - 186: 4.251 distance: 179 - 180: 5.479 distance: 179 - 187: 5.362 distance: 180 - 181: 3.531 distance: 181 - 191: 5.255 distance: 182 - 194: 3.844 distance: 196 - 197: 4.383 distance: 196 - 204: 6.666 distance: 197 - 198: 3.672 distance: 197 - 200: 6.910 distance: 198 - 199: 4.290 distance: 198 - 210: 4.392 distance: 199 - 254: 3.078 distance: 200 - 201: 4.481 distance: 200 - 206: 4.035 distance: 200 - 207: 5.017 distance: 201 - 203: 3.533 distance: 203 - 208: 3.010 distance: 211 - 212: 4.487 distance: 211 - 219: 5.997 distance: 212 - 213: 4.884 distance: 213 - 273: 7.851 distance: 215 - 217: 4.414 distance: 215 - 221: 6.702 distance: 215 - 222: 3.401 distance: 216 - 223: 4.891 distance: 216 - 224: 3.474 distance: 217 - 226: 3.116 distance: 217 - 228: 3.749 distance: 229 - 234: 5.944 distance: 230 - 233: 4.115 distance: 230 - 235: 5.348 distance: 231 - 232: 3.850 distance: 231 - 239: 4.484 distance: 232 - 297: 8.838 distance: 233 - 237: 4.846 distance: 233 - 238: 3.978 distance: 240 - 241: 3.497 distance: 240 - 243: 4.049 distance: 240 - 249: 4.915 distance: 242 - 319: 4.040 distance: 243 - 250: 4.188 distance: 244 - 245: 4.189 distance: 244 - 252: 4.443 distance: 244 - 253: 5.626 distance: 245 - 246: 3.294 distance: 254 - 262: 4.950 distance: 255 - 263: 3.723 distance: 257 - 335: 3.903 distance: 258 - 265: 3.621 distance: 259 - 266: 3.662 distance: 260 - 267: 3.424 distance: 273 - 274: 3.046 distance: 273 - 284: 3.417 distance: 275 - 276: 5.210 distance: 276 - 352: 6.900 distance: 277 - 278: 3.131 distance: 277 - 287: 5.807 distance: 278 - 289: 4.065 distance: 279 - 290: 3.068 distance: 280 - 281: 4.114 distance: 280 - 292: 3.525 distance: 281 - 282: 4.465