Starting phenix.real_space_refine (version: 1.21rc1) on Sun May 7 16:16:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/05_2023/6vxk_21442.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/05_2023/6vxk_21442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/05_2023/6vxk_21442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/05_2023/6vxk_21442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/05_2023/6vxk_21442.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/05_2023/6vxk_21442.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 10988 2.51 5 N 2960 2.21 5 O 3372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 668": "OE1" <-> "OE2" Residue "B ASP 704": "OD1" <-> "OD2" Residue "B PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D ARG 320": "NH1" <-> "NH2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "D PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "D ASP 704": "OD1" <-> "OD2" Residue "D PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 830": "OD1" <-> "OD2" Residue "D TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 17418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3022 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 361} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5561 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 714} Chain breaks: 12 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3022 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 361} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5561 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 714} Chain breaks: 12 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.99, per 1000 atoms: 0.52 Number of scatterers: 17418 At special positions: 0 Unit cell: (202.86, 101.844, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3372 8.00 N 2960 7.00 C 10988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 286 " distance=2.02 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 703 " distance=2.04 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 506 " distance=2.02 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 835 " distance=2.03 Simple disulfide: pdb=" SG CYS B 801 " - pdb=" SG CYS B 806 " distance=2.04 Simple disulfide: pdb=" SG CYS B 891 " - pdb=" SG CYS B 907 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 286 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 226 " - pdb=" SG CYS D 354 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 329 " distance=2.03 Simple disulfide: pdb=" SG CYS D 412 " - pdb=" SG CYS D 703 " distance=2.04 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 472 " distance=2.03 Simple disulfide: pdb=" SG CYS D 461 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 464 " - pdb=" SG CYS D 481 " distance=2.03 Simple disulfide: pdb=" SG CYS D 475 " - pdb=" SG CYS D 487 " distance=2.03 Simple disulfide: pdb=" SG CYS D 734 " - pdb=" SG CYS D 742 " distance=2.03 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 835 " distance=2.03 Simple disulfide: pdb=" SG CYS D 801 " - pdb=" SG CYS D 806 " distance=2.04 Simple disulfide: pdb=" SG CYS D 891 " - pdb=" SG CYS D 907 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 53 " " NAG B1601 " - " ASN B 141 " " NAG B1602 " - " ASN B 241 " " NAG B1603 " - " ASN B 149 " " NAG B1604 " - " ASN B 252 " " NAG B1605 " - " ASN B 86 " " NAG B1606 " - " ASN B 715 " " NAG B1607 " - " ASN B 771 " " NAG B1608 " - " ASN B 871 " " NAG C 501 " - " ASN C 53 " " NAG D1601 " - " ASN D 141 " " NAG D1602 " - " ASN D 241 " " NAG D1603 " - " ASN D 149 " " NAG D1604 " - " ASN D 252 " " NAG D1605 " - " ASN D 86 " " NAG D1606 " - " ASN D 715 " " NAG D1607 " - " ASN D 771 " " NAG D1608 " - " ASN D 871 " Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 2.5 seconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 50 sheets defined 5.2% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.715A pdb=" N SER A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 205' Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.547A pdb=" N CYS B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.747A pdb=" N CYS B 506 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.716A pdb=" N SER C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS C 205 " --> pdb=" O LEU C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 205' Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.547A pdb=" N CYS D 464 " --> pdb=" O SER D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 494 No H-bonds generated for 'chain 'D' and resid 492 through 494' Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.747A pdb=" N CYS D 506 " --> pdb=" O ALA D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 875 No H-bonds generated for 'chain 'D' and resid 873 through 875' Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.365A pdb=" N ILE A 64 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 78 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 162 removed outlier: 7.148A pdb=" N LYS A 212 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP A 309 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU A 214 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 218 removed outlier: 4.356A pdb=" N CYS A 217 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 234 removed outlier: 6.765A pdb=" N PHE A 244 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A 230 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A 242 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA A 232 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE A 240 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 332 Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.857A pdb=" N VAL B 430 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.605A pdb=" N SER B 77 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 112 Processing sheet with id=AB3, first strand: chain 'B' and resid 162 through 169 removed outlier: 4.957A pdb=" N ALA B 204 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY B 221 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N ASP B 209 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N GLU B 219 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AB5, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.290A pdb=" N ALA B 268 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE B 275 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL B 363 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER B 280 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 293 through 300 removed outlier: 6.511A pdb=" N VAL B 309 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER B 297 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 307 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU B 299 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 305 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 383 removed outlier: 6.435A pdb=" N LYS B 401 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL B 415 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB9, first strand: chain 'B' and resid 508 through 510 Processing sheet with id=AC1, first strand: chain 'B' and resid 546 through 548 Processing sheet with id=AC2, first strand: chain 'B' and resid 663 through 668 removed outlier: 3.729A pdb=" N TYR B 663 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR B 683 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 667 " --> pdb=" O ILE B 681 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 681 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE B 721 " --> pdb=" O ASN B 679 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 681 " --> pdb=" O MET B 719 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET B 719 " --> pdb=" O ILE B 681 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 671 through 673 removed outlier: 6.909A pdb=" N VAL B 672 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER B 744 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 735 " --> pdb=" O SER B 744 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 746 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 756 through 759 removed outlier: 3.630A pdb=" N GLY B 807 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 763 through 765 removed outlier: 5.140A pdb=" N TYR B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 828 " --> pdb=" O TYR B 832 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP B 834 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU B 826 " --> pdb=" O ASP B 834 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY B 836 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL B 824 " --> pdb=" O GLY B 836 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 846 through 849 Processing sheet with id=AC7, first strand: chain 'B' and resid 877 through 880 Processing sheet with id=AC8, first strand: chain 'C' and resid 14 through 19 Processing sheet with id=AC9, first strand: chain 'C' and resid 26 through 32 Processing sheet with id=AD1, first strand: chain 'C' and resid 63 through 66 removed outlier: 6.365A pdb=" N ILE C 64 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 78 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AD3, first strand: chain 'C' and resid 157 through 162 removed outlier: 7.148A pdb=" N LYS C 212 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP C 309 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 214 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 217 through 218 removed outlier: 4.357A pdb=" N CYS C 217 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 226 through 234 removed outlier: 6.766A pdb=" N PHE C 244 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 230 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR C 242 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA C 232 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE C 240 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 327 through 332 Processing sheet with id=AD7, first strand: chain 'D' and resid 39 through 41 removed outlier: 3.857A pdb=" N VAL D 430 " --> pdb=" O TYR D 440 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 48 through 51 removed outlier: 3.605A pdb=" N SER D 77 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 108 through 112 Processing sheet with id=AE1, first strand: chain 'D' and resid 162 through 169 removed outlier: 4.957A pdb=" N ALA D 204 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY D 221 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N ASP D 209 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N GLU D 219 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 231 through 234 Processing sheet with id=AE3, first strand: chain 'D' and resid 231 through 234 removed outlier: 6.290A pdb=" N ALA D 268 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE D 275 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL D 363 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER D 280 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 293 through 300 removed outlier: 6.512A pdb=" N VAL D 309 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 297 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA D 307 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU D 299 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 305 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 378 through 383 removed outlier: 6.435A pdb=" N LYS D 401 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL D 415 " --> pdb=" O LYS D 401 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 480 through 482 Processing sheet with id=AE7, first strand: chain 'D' and resid 508 through 510 Processing sheet with id=AE8, first strand: chain 'D' and resid 546 through 548 Processing sheet with id=AE9, first strand: chain 'D' and resid 663 through 668 removed outlier: 3.729A pdb=" N TYR D 663 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 683 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE D 667 " --> pdb=" O ILE D 681 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE D 681 " --> pdb=" O ILE D 667 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE D 721 " --> pdb=" O ASN D 679 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE D 681 " --> pdb=" O MET D 719 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET D 719 " --> pdb=" O ILE D 681 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 671 through 673 removed outlier: 6.909A pdb=" N VAL D 672 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER D 744 " --> pdb=" O ILE D 735 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE D 735 " --> pdb=" O SER D 744 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 746 " --> pdb=" O VAL D 733 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 756 through 759 removed outlier: 3.630A pdb=" N GLY D 807 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 763 through 765 removed outlier: 5.140A pdb=" N TYR D 832 " --> pdb=" O VAL D 828 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL D 828 " --> pdb=" O TYR D 832 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP D 834 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU D 826 " --> pdb=" O ASP D 834 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY D 836 " --> pdb=" O VAL D 824 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL D 824 " --> pdb=" O GLY D 836 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 846 through 849 Processing sheet with id=AF5, first strand: chain 'D' and resid 877 through 880 568 hydrogen bonds defined for protein. 1440 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: 7.21 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5558 1.33 - 1.45: 3598 1.45 - 1.58: 8484 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 17764 Sorted by residual: bond pdb=" C ILE A 311 " pdb=" N LYS A 312 " ideal model delta sigma weight residual 1.331 1.243 0.088 2.07e-02 2.33e+03 1.81e+01 bond pdb=" C ILE C 311 " pdb=" N LYS C 312 " ideal model delta sigma weight residual 1.331 1.243 0.088 2.07e-02 2.33e+03 1.79e+01 bond pdb=" CA ARG C 368 " pdb=" CB ARG C 368 " ideal model delta sigma weight residual 1.526 1.480 0.046 1.76e-02 3.23e+03 6.73e+00 bond pdb=" CA ARG A 368 " pdb=" CB ARG A 368 " ideal model delta sigma weight residual 1.526 1.481 0.045 1.76e-02 3.23e+03 6.62e+00 bond pdb=" CA SER C 252 " pdb=" CB SER C 252 " ideal model delta sigma weight residual 1.536 1.488 0.047 2.08e-02 2.31e+03 5.18e+00 ... (remaining 17759 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.46: 462 106.46 - 113.34: 10237 113.34 - 120.22: 5770 120.22 - 127.09: 7441 127.09 - 133.97: 200 Bond angle restraints: 24110 Sorted by residual: angle pdb=" C ASN B 411 " pdb=" N CYS B 412 " pdb=" CA CYS B 412 " ideal model delta sigma weight residual 120.67 112.83 7.84 1.34e+00 5.57e-01 3.43e+01 angle pdb=" C ASN D 411 " pdb=" N CYS D 412 " pdb=" CA CYS D 412 " ideal model delta sigma weight residual 120.67 112.83 7.84 1.34e+00 5.57e-01 3.43e+01 angle pdb=" CA CYS D 806 " pdb=" CB CYS D 806 " pdb=" SG CYS D 806 " ideal model delta sigma weight residual 114.40 126.17 -11.77 2.30e+00 1.89e-01 2.62e+01 angle pdb=" CA CYS B 806 " pdb=" CB CYS B 806 " pdb=" SG CYS B 806 " ideal model delta sigma weight residual 114.40 126.13 -11.73 2.30e+00 1.89e-01 2.60e+01 angle pdb=" N CYS D 801 " pdb=" CA CYS D 801 " pdb=" C CYS D 801 " ideal model delta sigma weight residual 109.52 117.32 -7.80 1.55e+00 4.16e-01 2.53e+01 ... (remaining 24105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9290 17.70 - 35.39: 1008 35.39 - 53.09: 194 53.09 - 70.79: 36 70.79 - 88.49: 16 Dihedral angle restraints: 10544 sinusoidal: 4052 harmonic: 6492 Sorted by residual: dihedral pdb=" CB CYS D 801 " pdb=" SG CYS D 801 " pdb=" SG CYS D 806 " pdb=" CB CYS D 806 " ideal model delta sinusoidal sigma weight residual 93.00 4.51 88.49 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS B 801 " pdb=" SG CYS B 801 " pdb=" SG CYS B 806 " pdb=" CB CYS B 806 " ideal model delta sinusoidal sigma weight residual 93.00 4.53 88.47 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS B 156 " pdb=" SG CYS B 156 " pdb=" SG CYS B 194 " pdb=" CB CYS B 194 " ideal model delta sinusoidal sigma weight residual -86.00 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 10541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2372 0.076 - 0.152: 411 0.152 - 0.228: 11 0.228 - 0.304: 4 0.304 - 0.380: 2 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 NAG D1608 " pdb=" ND2 ASN D 871 " pdb=" C2 NAG D1608 " pdb=" O5 NAG D1608 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B1608 " pdb=" ND2 ASN B 871 " pdb=" C2 NAG B1608 " pdb=" O5 NAG B1608 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B1603 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1603 " pdb=" O5 NAG B1603 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2797 not shown) Planarity restraints: 3086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 246 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO D 247 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 247 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 247 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 247 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 322 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO D 323 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 323 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 323 " -0.024 5.00e-02 4.00e+02 ... (remaining 3083 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 814 2.68 - 3.23: 16847 3.23 - 3.79: 27515 3.79 - 4.34: 36152 4.34 - 4.90: 62003 Nonbonded interactions: 143331 Sorted by model distance: nonbonded pdb=" O TRP B 175 " pdb=" OG1 THR B 210 " model vdw 2.122 2.440 nonbonded pdb=" O TRP D 175 " pdb=" OG1 THR D 210 " model vdw 2.122 2.440 nonbonded pdb=" O THR A 73 " pdb=" OG1 THR A 73 " model vdw 2.139 2.440 nonbonded pdb=" O THR C 73 " pdb=" OG1 THR C 73 " model vdw 2.139 2.440 nonbonded pdb=" OE2 GLU A 24 " pdb=" OH TYR A 45 " model vdw 2.160 2.440 ... (remaining 143326 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.370 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 47.830 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.011 0.088 17764 Z= 0.749 Angle : 0.841 11.770 24110 Z= 0.463 Chirality : 0.053 0.380 2800 Planarity : 0.004 0.047 3068 Dihedral : 14.735 87.569 6262 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer Outliers : 8.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.15), residues: 2198 helix: -2.73 (0.43), residues: 96 sheet: -1.59 (0.17), residues: 762 loop : -3.11 (0.13), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 69 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 95 residues processed: 208 average time/residue: 0.2563 time to fit residues: 87.5854 Evaluate side-chains 151 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 56 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.1630 time to fit residues: 31.8018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 264 HIS A 295 HIS B 67 GLN B 218 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 HIS B 670 GLN B 709 GLN B 718 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B 829 GLN C 80 ASN C 264 HIS C 295 HIS D 67 GLN D 218 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 HIS D 670 GLN D 709 GLN D 718 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN D 829 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17764 Z= 0.197 Angle : 0.605 10.060 24110 Z= 0.308 Chirality : 0.047 0.366 2800 Planarity : 0.004 0.043 3068 Dihedral : 5.004 21.107 2410 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.16), residues: 2198 helix: -1.79 (0.52), residues: 110 sheet: -1.10 (0.18), residues: 776 loop : -2.49 (0.15), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 64 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 9 residues processed: 96 average time/residue: 0.3580 time to fit residues: 51.2151 Evaluate side-chains 65 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 2.352 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1570 time to fit residues: 5.3775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 71.5636 > 50: distance: 24 - 28: 29.824 distance: 28 - 29: 32.842 distance: 29 - 30: 8.782 distance: 29 - 32: 8.406 distance: 30 - 35: 40.105 distance: 32 - 33: 5.236 distance: 35 - 36: 21.237 distance: 36 - 37: 16.185 distance: 36 - 39: 43.259 distance: 37 - 41: 20.972 distance: 39 - 40: 56.433 distance: 41 - 42: 39.267 distance: 42 - 43: 47.414 distance: 42 - 45: 10.368 distance: 43 - 44: 31.470 distance: 43 - 48: 38.741 distance: 45 - 46: 35.529 distance: 49 - 52: 39.360 distance: 50 - 51: 39.468 distance: 52 - 53: 40.546 distance: 56 - 57: 56.247 distance: 58 - 59: 56.907 distance: 58 - 60: 32.607 distance: 60 - 61: 40.765 distance: 60 - 136: 30.143 distance: 61 - 62: 69.402 distance: 61 - 64: 39.265 distance: 62 - 63: 38.917 distance: 62 - 69: 41.053 distance: 63 - 133: 34.394 distance: 64 - 65: 40.790 distance: 65 - 66: 40.108 distance: 67 - 68: 39.625 distance: 70 - 71: 24.517 distance: 70 - 73: 39.852 distance: 71 - 72: 31.876 distance: 71 - 75: 15.400 distance: 73 - 74: 56.447 distance: 75 - 76: 48.020 distance: 75 - 123: 29.068 distance: 76 - 77: 55.135 distance: 76 - 79: 57.145 distance: 77 - 78: 55.759 distance: 77 - 83: 57.180 distance: 79 - 80: 18.481 distance: 80 - 81: 4.496 distance: 80 - 82: 19.559 distance: 83 - 84: 46.541 distance: 84 - 85: 42.633 distance: 84 - 87: 26.497 distance: 85 - 86: 38.926 distance: 85 - 90: 59.136 distance: 87 - 88: 25.285 distance: 87 - 89: 11.067 distance: 90 - 91: 48.978 distance: 91 - 92: 41.621 distance: 91 - 94: 45.080 distance: 92 - 93: 9.536 distance: 92 - 98: 34.415 distance: 94 - 95: 38.411 distance: 94 - 96: 51.872 distance: 95 - 97: 44.347