Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 08:00:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/10_2023/5u6o_8511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/10_2023/5u6o_8511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/10_2023/5u6o_8511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/10_2023/5u6o_8511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/10_2023/5u6o_8511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/10_2023/5u6o_8511.pdb" } resolution = 3.5 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= 0.006 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 108 5.16 5 C 9432 2.51 5 N 2448 2.21 5 O 2492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 404": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 14480 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3620 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 16, 'TRANS': 465} Chain breaks: 2 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 166 Chain: "B" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3620 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 16, 'TRANS': 465} Chain breaks: 2 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 166 Chain: "C" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3620 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 16, 'TRANS': 465} Chain breaks: 2 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 166 Chain: "D" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3620 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 16, 'TRANS': 465} Chain breaks: 2 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 166 Time building chain proxies: 7.88, per 1000 atoms: 0.54 Number of scatterers: 14480 At special positions: 0 Unit cell: (123.5, 123.5, 115.7, 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 108 16.00 O 2492 8.00 N 2448 7.00 C 9432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.31 Conformation dependent library (CDL) restraints added in 2.4 seconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 71.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 removed outlier: 4.104A pdb=" N PHE A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 167 removed outlier: 3.724A pdb=" N GLY A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.563A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.687A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.191A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.587A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 422 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 473 removed outlier: 5.694A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.503A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.794A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.665A pdb=" N THR B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 167 removed outlier: 3.724A pdb=" N GLY B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 3.565A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.688A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.191A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.584A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 422 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 473 removed outlier: 5.693A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.504A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.794A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 585 Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.665A pdb=" N THR C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 167 removed outlier: 3.724A pdb=" N GLY C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Proline residue: C 161 - end of helix removed outlier: 3.565A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.687A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.193A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.587A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 422 Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 473 removed outlier: 5.692A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 491 removed outlier: 3.503A pdb=" N LYS C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.793A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 585 Processing helix chain 'D' and resid 95 through 103 removed outlier: 3.664A pdb=" N THR D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 167 removed outlier: 3.724A pdb=" N GLY D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Proline residue: D 161 - end of helix removed outlier: 3.564A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.687A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.190A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.585A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 422 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 473 removed outlier: 5.695A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 491 removed outlier: 3.504A pdb=" N LYS D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.794A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.602A pdb=" N ARG A 554 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 522 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP A 556 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 520 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR A 558 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 518 " --> pdb=" O TYR A 558 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 516 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.556A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A 554 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 522 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP A 556 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 520 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR A 558 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 518 " --> pdb=" O TYR A 558 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 516 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.601A pdb=" N ARG B 554 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL B 522 " --> pdb=" O ARG B 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP B 556 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 520 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYR B 558 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY B 518 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 516 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.558A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG B 554 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL B 522 " --> pdb=" O ARG B 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP B 556 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 520 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYR B 558 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY B 518 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 516 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.602A pdb=" N ARG C 554 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL C 522 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP C 556 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 520 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR C 558 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY C 518 " --> pdb=" O TYR C 558 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 516 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.557A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG C 554 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL C 522 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP C 556 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 520 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR C 558 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY C 518 " --> pdb=" O TYR C 558 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 516 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.602A pdb=" N ARG D 554 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 522 " --> pdb=" O ARG D 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP D 556 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA D 520 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR D 558 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY D 518 " --> pdb=" O TYR D 558 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 516 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.558A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG D 554 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 522 " --> pdb=" O ARG D 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP D 556 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA D 520 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR D 558 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY D 518 " --> pdb=" O TYR D 558 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 516 " --> pdb=" O ARG D 560 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 3096 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: 4.48 Time building geometry restraints manager: 6.72 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: 2609 1.33 - 1.45: 3919 1.45 - 1.57: 8124 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 14840 Sorted by residual: bond pdb=" C ASN B 300 " pdb=" O ASN B 300 " ideal model delta sigma weight residual 1.236 1.273 -0.036 1.15e-02 7.56e+03 9.90e+00 bond pdb=" C ASN D 300 " pdb=" O ASN D 300 " ideal model delta sigma weight residual 1.236 1.272 -0.035 1.15e-02 7.56e+03 9.50e+00 bond pdb=" C ASN C 300 " pdb=" O ASN C 300 " ideal model delta sigma weight residual 1.236 1.271 -0.035 1.15e-02 7.56e+03 9.19e+00 bond pdb=" C ASN A 300 " pdb=" O ASN A 300 " ideal model delta sigma weight residual 1.236 1.271 -0.035 1.15e-02 7.56e+03 9.06e+00 bond pdb=" C LEU D 306 " pdb=" O LEU D 306 " ideal model delta sigma weight residual 1.236 1.269 -0.032 1.15e-02 7.56e+03 7.86e+00 ... (remaining 14835 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.48: 402 106.48 - 113.42: 7603 113.42 - 120.36: 5659 120.36 - 127.30: 6379 127.30 - 134.23: 141 Bond angle restraints: 20184 Sorted by residual: angle pdb=" O VAL C 319 " pdb=" C VAL C 319 " pdb=" N PRO C 320 " ideal model delta sigma weight residual 120.07 124.19 -4.12 7.10e-01 1.98e+00 3.37e+01 angle pdb=" O VAL B 319 " pdb=" C VAL B 319 " pdb=" N PRO B 320 " ideal model delta sigma weight residual 120.07 124.18 -4.11 7.10e-01 1.98e+00 3.35e+01 angle pdb=" O VAL A 319 " pdb=" C VAL A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 120.07 124.17 -4.10 7.10e-01 1.98e+00 3.34e+01 angle pdb=" O VAL D 319 " pdb=" C VAL D 319 " pdb=" N PRO D 320 " ideal model delta sigma weight residual 120.07 124.16 -4.09 7.10e-01 1.98e+00 3.31e+01 angle pdb=" O ASP D 455 " pdb=" C ASP D 455 " pdb=" N PRO D 456 " ideal model delta sigma weight residual 120.38 124.75 -4.37 7.90e-01 1.60e+00 3.06e+01 ... (remaining 20179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 8052 16.18 - 32.36: 544 32.36 - 48.54: 68 48.54 - 64.72: 16 64.72 - 80.91: 4 Dihedral angle restraints: 8684 sinusoidal: 3008 harmonic: 5676 Sorted by residual: dihedral pdb=" CA ASN D 465 " pdb=" C ASN D 465 " pdb=" N CYS D 466 " pdb=" CA CYS D 466 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASN A 465 " pdb=" C ASN A 465 " pdb=" N CYS A 466 " pdb=" CA CYS A 466 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASN C 465 " pdb=" C ASN C 465 " pdb=" N CYS C 466 " pdb=" CA CYS C 466 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 8681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1474 0.065 - 0.129: 553 0.129 - 0.194: 189 0.194 - 0.258: 39 0.258 - 0.323: 13 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA PHE D 186 " pdb=" N PHE D 186 " pdb=" C PHE D 186 " pdb=" CB PHE D 186 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA PHE C 186 " pdb=" N PHE C 186 " pdb=" C PHE C 186 " pdb=" CB PHE C 186 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA PHE B 186 " pdb=" N PHE B 186 " pdb=" C PHE B 186 " pdb=" CB PHE B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2265 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 319 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 320 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 319 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B 320 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO D 320 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " -0.056 5.00e-02 4.00e+02 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5244 2.88 - 3.39: 15227 3.39 - 3.89: 24506 3.89 - 4.40: 26984 4.40 - 4.90: 43744 Nonbonded interactions: 115705 Sorted by model distance: nonbonded pdb=" O VAL A 257 " pdb=" OG1 THR A 260 " model vdw 2.380 2.440 nonbonded pdb=" O VAL C 257 " pdb=" OG1 THR C 260 " model vdw 2.381 2.440 nonbonded pdb=" O VAL D 257 " pdb=" OG1 THR D 260 " model vdw 2.381 2.440 nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 260 " model vdw 2.381 2.440 nonbonded pdb=" O LYS A 261 " pdb=" OG SER A 264 " model vdw 2.415 2.440 ... (remaining 115700 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 4.640 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 41.010 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 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 : 0.008 0.042 14840 Z= 0.499 Angle : 1.441 6.963 20184 Z= 1.117 Chirality : 0.077 0.323 2268 Planarity : 0.006 0.104 2564 Dihedral : 11.339 80.905 5012 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 1904 helix: 2.21 (0.12), residues: 1276 sheet: -3.72 (0.34), residues: 116 loop : -2.35 (0.21), residues: 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 1.699 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2641 time to fit residues: 174.7136 Evaluate side-chains 293 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 421 HIS B 398 GLN B 421 HIS C 286 HIS C 398 GLN C 421 HIS D 398 GLN D 421 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14840 Z= 0.278 Angle : 0.602 8.611 20184 Z= 0.325 Chirality : 0.042 0.173 2268 Planarity : 0.005 0.058 2564 Dihedral : 4.173 19.308 2076 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.87 % Allowed : 9.40 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.19), residues: 1904 helix: 3.18 (0.14), residues: 1304 sheet: -2.72 (0.40), residues: 112 loop : -1.88 (0.24), residues: 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 346 time to evaluate : 1.824 Fit side-chains outliers start: 25 outliers final: 16 residues processed: 362 average time/residue: 0.2179 time to fit residues: 122.5639 Evaluate side-chains 282 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 266 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1309 time to fit residues: 6.2161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 188 optimal weight: 20.0000 chunk 155 optimal weight: 0.5980 chunk 173 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 300 ASN A 568 ASN B 156 ASN B 300 ASN B 568 ASN C 156 ASN C 300 ASN C 568 ASN D 156 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN D 568 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14840 Z= 0.264 Angle : 0.552 6.222 20184 Z= 0.301 Chirality : 0.043 0.213 2268 Planarity : 0.004 0.046 2564 Dihedral : 4.067 18.662 2076 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.19 % Allowed : 12.24 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1904 helix: 2.84 (0.14), residues: 1304 sheet: -2.06 (0.43), residues: 112 loop : -1.62 (0.25), residues: 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 320 time to evaluate : 1.600 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 327 average time/residue: 0.2137 time to fit residues: 109.2575 Evaluate side-chains 290 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 285 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1246 time to fit residues: 3.4016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 166 optimal weight: 0.0270 chunk 50 optimal weight: 7.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14840 Z= 0.187 Angle : 0.517 7.846 20184 Z= 0.278 Chirality : 0.041 0.221 2268 Planarity : 0.004 0.038 2564 Dihedral : 3.937 17.106 2076 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.49 % Allowed : 14.33 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 1904 helix: 2.63 (0.14), residues: 1304 sheet: -1.89 (0.43), residues: 120 loop : -1.39 (0.26), residues: 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 319 time to evaluate : 1.467 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 329 average time/residue: 0.2165 time to fit residues: 111.2108 Evaluate side-chains 285 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1329 time to fit residues: 3.9585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 138 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14840 Z= 0.259 Angle : 0.529 7.160 20184 Z= 0.288 Chirality : 0.042 0.203 2268 Planarity : 0.004 0.037 2564 Dihedral : 3.937 17.559 2076 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.01 % Allowed : 14.48 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.19), residues: 1904 helix: 2.43 (0.14), residues: 1312 sheet: -1.49 (0.44), residues: 120 loop : -1.26 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 299 time to evaluate : 1.737 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 309 average time/residue: 0.2099 time to fit residues: 102.5608 Evaluate side-chains 295 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 279 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1262 time to fit residues: 6.1195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14840 Z= 0.333 Angle : 0.585 8.520 20184 Z= 0.312 Chirality : 0.043 0.191 2268 Planarity : 0.004 0.033 2564 Dihedral : 4.080 17.322 2076 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 15.75 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 1904 helix: 2.27 (0.14), residues: 1308 sheet: -1.25 (0.45), residues: 120 loop : -1.22 (0.26), residues: 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 278 time to evaluate : 1.875 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 289 average time/residue: 0.2131 time to fit residues: 97.2884 Evaluate side-chains 285 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 264 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1264 time to fit residues: 7.2531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14840 Z= 0.170 Angle : 0.506 7.929 20184 Z= 0.271 Chirality : 0.040 0.229 2268 Planarity : 0.003 0.030 2564 Dihedral : 3.894 17.991 2076 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.82 % Allowed : 17.69 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 1904 helix: 2.28 (0.14), residues: 1312 sheet: -0.94 (0.46), residues: 120 loop : -0.93 (0.28), residues: 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 310 time to evaluate : 1.738 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 311 average time/residue: 0.2138 time to fit residues: 104.4558 Evaluate side-chains 284 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1441 time to fit residues: 3.5910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14840 Z= 0.173 Angle : 0.533 7.821 20184 Z= 0.283 Chirality : 0.041 0.189 2268 Planarity : 0.003 0.035 2564 Dihedral : 3.913 19.415 2076 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.82 % Allowed : 18.28 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 1904 helix: 2.27 (0.14), residues: 1308 sheet: -0.76 (0.46), residues: 120 loop : -0.76 (0.27), residues: 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 293 time to evaluate : 1.833 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 297 average time/residue: 0.1967 time to fit residues: 95.2756 Evaluate side-chains 279 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1302 time to fit residues: 3.5728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14840 Z= 0.173 Angle : 0.545 16.420 20184 Z= 0.285 Chirality : 0.040 0.185 2268 Planarity : 0.003 0.034 2564 Dihedral : 3.875 19.990 2076 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.60 % Allowed : 19.33 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.19), residues: 1904 helix: 2.32 (0.14), residues: 1304 sheet: -0.72 (0.45), residues: 120 loop : -0.71 (0.27), residues: 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 283 time to evaluate : 1.784 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 285 average time/residue: 0.2002 time to fit residues: 92.1412 Evaluate side-chains 280 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 278 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1303 time to fit residues: 2.7283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14840 Z= 0.220 Angle : 0.547 11.094 20184 Z= 0.291 Chirality : 0.041 0.186 2268 Planarity : 0.003 0.034 2564 Dihedral : 3.907 19.866 2076 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.30 % Allowed : 19.70 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.19), residues: 1904 helix: 2.26 (0.14), residues: 1308 sheet: -0.63 (0.45), residues: 120 loop : -0.63 (0.28), residues: 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 280 time to evaluate : 1.566 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 282 average time/residue: 0.2017 time to fit residues: 92.2678 Evaluate side-chains 275 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 273 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1308 time to fit residues: 2.8387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 22 optimal weight: 0.3980 chunk 42 optimal weight: 20.0000 chunk 152 optimal weight: 0.5980 chunk 63 optimal weight: 0.0670 chunk 156 optimal weight: 0.0470 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 133 optimal weight: 0.0270 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 286 HIS A 300 ASN B 179 ASN C 179 ASN D 286 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090309 restraints weight = 34195.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090419 restraints weight = 18650.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091265 restraints weight = 15357.807| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14840 Z= 0.146 Angle : 0.537 12.070 20184 Z= 0.279 Chirality : 0.040 0.202 2268 Planarity : 0.003 0.035 2564 Dihedral : 3.800 20.867 2076 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.37 % Allowed : 20.30 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 1904 helix: 2.36 (0.14), residues: 1304 sheet: -0.42 (0.45), residues: 120 loop : -0.55 (0.28), residues: 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2776.61 seconds wall clock time: 51 minutes 24.47 seconds (3084.47 seconds total)