Starting phenix.real_space_refine on Mon Dec 11 10:07:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/12_2023/6vxk_21442.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/12_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_21442/12_2023/6vxk_21442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/12_2023/6vxk_21442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/12_2023/6vxk_21442.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxk_21442/12_2023/6vxk_21442.pdb" } resolution = 3.1 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= 0.000 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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 dihedrals: 3 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 dihedrals: 24 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 dihedrals: 3 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 9.51, per 1000 atoms: 0.55 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: 7.05 Conformation dependent library (CDL) restraints added in 3.2 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: 2.38 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: 7.38 Time building geometry restraints manager: 7.58 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: 9612 17.70 - 35.39: 1032 35.39 - 53.09: 216 53.09 - 70.79: 46 70.79 - 88.49: 16 Dihedral angle restraints: 10922 sinusoidal: 4430 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 10919 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 10.730 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 49.720 Find NCS groups from input model: 1.070 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.170 ------------------------------------------------------------------------------- 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 : 14.805 87.569 6640 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 % Allowed : 17.01 % Favored : 74.95 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 765 HIS 0.006 0.001 HIS C 337 PHE 0.020 0.002 PHE C 344 TYR 0.016 0.002 TYR A 351 ARG 0.005 0.001 ARG C 222 *********************** 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 : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 95 residues processed: 208 average time/residue: 0.2467 time to fit residues: 84.0300 Evaluate side-chains 151 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 56 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.1633 time to fit residues: 31.8043 ------------------------------------------------------------------------------- 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 C 348 ASN 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17764 Z= 0.192 Angle : 0.598 10.167 24110 Z= 0.306 Chirality : 0.047 0.398 2800 Planarity : 0.004 0.044 3068 Dihedral : 6.850 57.943 2788 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.16 % Allowed : 21.44 % Favored : 76.40 % 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: -2.81 (0.16), residues: 2198 helix: -1.73 (0.53), residues: 110 sheet: -1.13 (0.18), residues: 770 loop : -2.44 (0.15), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 765 HIS 0.003 0.001 HIS D 755 PHE 0.015 0.001 PHE C 344 TYR 0.012 0.001 TYR C 351 ARG 0.002 0.000 ARG D 291 *********************** 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 102 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 62 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 12 residues processed: 98 average time/residue: 0.3641 time to fit residues: 53.4717 Evaluate side-chains 69 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1604 time to fit residues: 6.4954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 50.0000 chunk 181 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17764 Z= 0.231 Angle : 0.592 11.144 24110 Z= 0.301 Chirality : 0.047 0.381 2800 Planarity : 0.004 0.042 3068 Dihedral : 6.117 59.482 2788 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.48 % Allowed : 22.19 % Favored : 75.32 % 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: -2.38 (0.17), residues: 2198 helix: -1.46 (0.54), residues: 110 sheet: -0.85 (0.18), residues: 774 loop : -2.12 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 765 HIS 0.001 0.000 HIS D 233 PHE 0.017 0.001 PHE A 344 TYR 0.012 0.001 TYR C 351 ARG 0.009 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 3 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 107 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 61 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 20 residues processed: 100 average time/residue: 0.3124 time to fit residues: 49.1407 Evaluate side-chains 74 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1607 time to fit residues: 8.7309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 193 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS B 353 HIS ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS D 353 HIS ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 17764 Z= 0.515 Angle : 0.676 9.435 24110 Z= 0.345 Chirality : 0.049 0.373 2800 Planarity : 0.004 0.039 3068 Dihedral : 6.284 54.799 2788 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.38 % Allowed : 22.52 % Favored : 75.11 % 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: -2.37 (0.17), residues: 2198 helix: -1.49 (0.54), residues: 110 sheet: -0.88 (0.18), residues: 788 loop : -2.10 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 327 HIS 0.004 0.001 HIS D 157 PHE 0.021 0.002 PHE A 344 TYR 0.017 0.002 TYR C 351 ARG 0.006 0.001 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 4 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: 44 poor density : 56 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 98 average time/residue: 0.2803 time to fit residues: 45.0925 Evaluate side-chains 83 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 54 time to evaluate : 2.149 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1615 time to fit residues: 11.7782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17764 Z= 0.274 Angle : 0.588 9.587 24110 Z= 0.300 Chirality : 0.046 0.359 2800 Planarity : 0.004 0.036 3068 Dihedral : 5.775 58.438 2788 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.24 % Allowed : 23.65 % Favored : 75.11 % 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: -2.19 (0.17), residues: 2198 helix: -1.40 (0.53), residues: 110 sheet: -0.76 (0.18), residues: 798 loop : -1.98 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 207 HIS 0.002 0.000 HIS B 157 PHE 0.024 0.002 PHE D 760 TYR 0.013 0.001 TYR C 351 ARG 0.005 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 5 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 78 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 55 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 75 average time/residue: 0.3389 time to fit residues: 40.2985 Evaluate side-chains 64 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 2.184 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1844 time to fit residues: 6.5417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 chunk 216 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 100 optimal weight: 0.0270 chunk 18 optimal weight: 0.3980 chunk 71 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17764 Z= 0.165 Angle : 0.538 9.645 24110 Z= 0.273 Chirality : 0.046 0.351 2800 Planarity : 0.003 0.037 3068 Dihedral : 5.192 56.628 2788 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.08 % Allowed : 23.54 % Favored : 75.38 % 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: -1.98 (0.17), residues: 2198 helix: -1.18 (0.54), residues: 110 sheet: -0.59 (0.18), residues: 800 loop : -1.86 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 765 HIS 0.001 0.000 HIS A 114 PHE 0.022 0.001 PHE B 760 TYR 0.016 0.001 TYR D 663 ARG 0.006 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 6 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 83 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 2.120 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 83 average time/residue: 0.2894 time to fit residues: 39.3487 Evaluate side-chains 62 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1619 time to fit residues: 4.4824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 215 optimal weight: 0.3980 chunk 135 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 0.0060 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17764 Z= 0.175 Angle : 0.535 9.644 24110 Z= 0.271 Chirality : 0.045 0.333 2800 Planarity : 0.003 0.035 3068 Dihedral : 5.097 57.389 2788 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.86 % Allowed : 24.30 % Favored : 74.84 % 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: -1.80 (0.17), residues: 2198 helix: -1.03 (0.54), residues: 110 sheet: -0.46 (0.19), residues: 788 loop : -1.74 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 765 HIS 0.001 0.000 HIS B 471 PHE 0.021 0.001 PHE B 760 TYR 0.010 0.001 TYR C 351 ARG 0.003 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 7 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 75 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 73 average time/residue: 0.3163 time to fit residues: 37.8984 Evaluate side-chains 64 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 2.083 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1616 time to fit residues: 4.6318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17764 Z= 0.313 Angle : 0.586 9.575 24110 Z= 0.298 Chirality : 0.047 0.325 2800 Planarity : 0.004 0.034 3068 Dihedral : 5.407 59.041 2788 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.76 % Allowed : 24.78 % Favored : 74.46 % 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: -1.80 (0.17), residues: 2198 helix: -1.09 (0.54), residues: 110 sheet: -0.47 (0.19), residues: 788 loop : -1.73 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 327 HIS 0.003 0.001 HIS D 157 PHE 0.027 0.002 PHE B 760 TYR 0.017 0.001 TYR D 663 ARG 0.003 0.000 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 8 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 67 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 2.142 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.3381 time to fit residues: 35.4366 Evaluate side-chains 62 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 2.181 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1693 time to fit residues: 5.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.0070 chunk 206 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 201 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 chunk 87 optimal weight: 50.0000 chunk 157 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 200 optimal weight: 30.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17764 Z= 0.270 Angle : 0.572 9.579 24110 Z= 0.291 Chirality : 0.046 0.320 2800 Planarity : 0.003 0.034 3068 Dihedral : 5.375 59.713 2788 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.22 % Allowed : 24.84 % Favored : 74.95 % 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: -1.79 (0.17), residues: 2198 helix: -1.06 (0.54), residues: 110 sheet: -0.47 (0.18), residues: 808 loop : -1.73 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 327 HIS 0.002 0.000 HIS D 755 PHE 0.028 0.002 PHE B 760 TYR 0.013 0.001 TYR C 351 ARG 0.003 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 9 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 58 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 2.122 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.3425 time to fit residues: 31.0225 Evaluate side-chains 55 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1764 time to fit residues: 3.6246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17764 Z= 0.227 Angle : 0.561 9.580 24110 Z= 0.286 Chirality : 0.046 0.319 2800 Planarity : 0.003 0.034 3068 Dihedral : 5.291 59.459 2788 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.27 % Allowed : 24.89 % Favored : 74.84 % 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: -1.74 (0.17), residues: 2198 helix: -0.99 (0.55), residues: 110 sheet: -0.43 (0.19), residues: 808 loop : -1.70 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 765 HIS 0.014 0.001 HIS A 337 PHE 0.029 0.001 PHE B 760 TYR 0.017 0.001 TYR B 663 ARG 0.003 0.000 ARG B 332 ********************** REFINEMENT MACRO_CYCLE 10 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 61 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 2.354 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.3151 time to fit residues: 31.1769 Evaluate side-chains 56 residues out of total 1966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1643 time to fit residues: 3.3500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 56.1516 > 50: distance: 113 - 117: 11.606 distance: 117 - 118: 8.795 distance: 118 - 119: 16.184 distance: 118 - 121: 9.445 distance: 119 - 120: 3.694 distance: 119 - 126: 5.789 distance: 121 - 122: 12.077 distance: 122 - 123: 15.480 distance: 123 - 124: 14.776 distance: 123 - 125: 29.987 distance: 126 - 127: 43.093 distance: 127 - 128: 10.283 distance: 128 - 129: 20.113 distance: 128 - 130: 8.300 distance: 130 - 131: 18.726 distance: 131 - 132: 22.141 distance: 131 - 134: 9.802 distance: 132 - 133: 23.082 distance: 132 - 138: 23.436 distance: 134 - 135: 10.845 distance: 135 - 136: 13.744 distance: 135 - 137: 29.980 distance: 138 - 139: 18.212 distance: 139 - 140: 13.192 distance: 139 - 142: 14.356 distance: 140 - 141: 10.806 distance: 140 - 147: 10.711 distance: 142 - 143: 27.645 distance: 143 - 144: 25.238 distance: 144 - 145: 21.911 distance: 144 - 146: 20.217 distance: 147 - 148: 8.909 distance: 147 - 153: 11.090 distance: 148 - 149: 8.743 distance: 148 - 151: 17.963 distance: 149 - 150: 7.138 distance: 149 - 154: 8.697 distance: 151 - 152: 23.611 distance: 152 - 153: 10.039 distance: 154 - 155: 12.918 distance: 155 - 156: 14.008 distance: 155 - 158: 14.196 distance: 156 - 157: 4.976 distance: 156 - 163: 27.324 distance: 158 - 159: 22.716 distance: 159 - 160: 16.801 distance: 160 - 161: 26.792 distance: 160 - 162: 17.059 distance: 163 - 164: 15.380 distance: 164 - 165: 13.748 distance: 164 - 167: 16.964 distance: 165 - 166: 4.965 distance: 165 - 174: 22.927 distance: 167 - 168: 16.484 distance: 168 - 169: 13.391 distance: 169 - 170: 17.183 distance: 170 - 171: 5.193 distance: 171 - 172: 18.715 distance: 171 - 173: 22.540 distance: 174 - 175: 16.242 distance: 175 - 176: 19.503 distance: 175 - 178: 12.780 distance: 176 - 177: 36.715 distance: 176 - 181: 17.631 distance: 178 - 179: 5.761 distance: 178 - 180: 34.811 distance: 181 - 182: 8.797 distance: 182 - 183: 10.698 distance: 182 - 185: 5.682 distance: 183 - 184: 22.381 distance: 183 - 190: 17.618 distance: 186 - 187: 9.242 distance: 187 - 188: 30.671 distance: 187 - 189: 40.957 distance: 190 - 191: 15.775 distance: 190 - 196: 25.477 distance: 191 - 192: 9.113 distance: 191 - 194: 15.530 distance: 192 - 193: 13.944 distance: 192 - 197: 14.242 distance: 194 - 195: 31.525 distance: 195 - 196: 9.908