Starting phenix.real_space_refine on Sat Mar 16 10:54:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/03_2024/5u6o_8511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/03_2024/5u6o_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_8511/03_2024/5u6o_8511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/03_2024/5u6o_8511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/03_2024/5u6o_8511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6o_8511/03_2024/5u6o_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-dev-5265/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: 7.55, per 1000 atoms: 0.52 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: 5.23 Conformation dependent library (CDL) restraints added in 2.6 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: 1.31 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: 4.54 Time building geometry restraints manager: 5.74 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: 0.970 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: 0.010 Extract box with map and model: 4.550 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 37.520 Find NCS groups from input model: 0.900 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.870 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 281 HIS 0.006 0.003 HIS A 392 PHE 0.028 0.002 PHE B 186 TYR 0.028 0.003 TYR C 411 ARG 0.005 0.001 ARG C 267 *********************** 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 : 1.617 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8013 (mm-30) REVERT: A 122 LYS cc_start: 0.9078 (tttt) cc_final: 0.8820 (tptp) REVERT: A 149 MET cc_start: 0.8434 (mmm) cc_final: 0.8140 (mmm) REVERT: A 189 ASP cc_start: 0.8732 (t0) cc_final: 0.8375 (t0) REVERT: A 283 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8030 (tp30) REVERT: A 317 PHE cc_start: 0.8034 (t80) cc_final: 0.7809 (t80) REVERT: A 433 ASP cc_start: 0.8078 (m-30) cc_final: 0.7848 (m-30) REVERT: A 445 ASP cc_start: 0.6910 (t0) cc_final: 0.6664 (t0) REVERT: A 515 ILE cc_start: 0.7728 (mt) cc_final: 0.7353 (tt) REVERT: A 517 HIS cc_start: 0.6518 (t70) cc_final: 0.5785 (t-90) REVERT: B 101 MET cc_start: 0.7359 (mmm) cc_final: 0.7098 (ttm) REVERT: B 113 MET cc_start: 0.8803 (tpp) cc_final: 0.8393 (mmm) REVERT: B 121 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8067 (mm-30) REVERT: B 149 MET cc_start: 0.8421 (mmm) cc_final: 0.8103 (mmm) REVERT: B 189 ASP cc_start: 0.8824 (t0) cc_final: 0.8508 (t70) REVERT: B 282 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 283 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8068 (tp30) REVERT: B 287 MET cc_start: 0.6209 (mmm) cc_final: 0.5938 (tpt) REVERT: B 317 PHE cc_start: 0.7963 (t80) cc_final: 0.7749 (t80) REVERT: B 356 MET cc_start: 0.7555 (ttm) cc_final: 0.7354 (ttt) REVERT: B 433 ASP cc_start: 0.8113 (m-30) cc_final: 0.7858 (m-30) REVERT: B 445 ASP cc_start: 0.7080 (t0) cc_final: 0.6804 (t0) REVERT: B 515 ILE cc_start: 0.7720 (mt) cc_final: 0.7299 (tt) REVERT: B 517 HIS cc_start: 0.6585 (t70) cc_final: 0.5878 (t-90) REVERT: C 101 MET cc_start: 0.7412 (mmm) cc_final: 0.7144 (ttm) REVERT: C 121 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8042 (mm-30) REVERT: C 122 LYS cc_start: 0.9039 (tttt) cc_final: 0.8769 (tptp) REVERT: C 149 MET cc_start: 0.8418 (mmm) cc_final: 0.8113 (mmm) REVERT: C 189 ASP cc_start: 0.8740 (t0) cc_final: 0.8451 (t70) REVERT: C 283 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7894 (tp30) REVERT: C 317 PHE cc_start: 0.7994 (t80) cc_final: 0.7762 (t80) REVERT: C 356 MET cc_start: 0.7545 (ttm) cc_final: 0.7338 (ttt) REVERT: C 433 ASP cc_start: 0.8057 (m-30) cc_final: 0.7781 (m-30) REVERT: C 445 ASP cc_start: 0.7206 (t0) cc_final: 0.6975 (t0) REVERT: C 494 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6908 (mt-10) REVERT: C 515 ILE cc_start: 0.7814 (mt) cc_final: 0.7384 (tt) REVERT: C 517 HIS cc_start: 0.6459 (t70) cc_final: 0.5734 (t-90) REVERT: D 121 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8020 (mm-30) REVERT: D 122 LYS cc_start: 0.9065 (tttt) cc_final: 0.8801 (tptp) REVERT: D 149 MET cc_start: 0.8419 (mmm) cc_final: 0.8133 (mmm) REVERT: D 189 ASP cc_start: 0.8718 (t0) cc_final: 0.8382 (t0) REVERT: D 278 ILE cc_start: 0.7738 (mm) cc_final: 0.7536 (mt) REVERT: D 282 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7789 (mt-10) REVERT: D 283 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7949 (tp30) REVERT: D 317 PHE cc_start: 0.8029 (t80) cc_final: 0.7778 (t80) REVERT: D 433 ASP cc_start: 0.8037 (m-30) cc_final: 0.7770 (m-30) REVERT: D 445 ASP cc_start: 0.6979 (t0) cc_final: 0.6744 (t0) REVERT: D 494 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6841 (mt-10) REVERT: D 515 ILE cc_start: 0.7758 (mt) cc_final: 0.7369 (tt) REVERT: D 517 HIS cc_start: 0.6438 (t70) cc_final: 0.5714 (t-90) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2405 time to fit residues: 158.6939 Evaluate side-chains 323 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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: 0.6980 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 0.0050 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.3400 ------------------------------------------------------------------------------- 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 398 GLN C 421 HIS D 398 GLN D 421 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14840 Z= 0.322 Angle : 0.596 7.942 20184 Z= 0.319 Chirality : 0.042 0.159 2268 Planarity : 0.005 0.058 2564 Dihedral : 4.229 20.246 2076 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.94 % Allowed : 8.43 % Favored : 89.63 % 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: 2.38 (0.19), residues: 1904 helix: 3.13 (0.14), residues: 1300 sheet: -2.72 (0.40), residues: 112 loop : -1.86 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 330 HIS 0.006 0.002 HIS C 392 PHE 0.024 0.002 PHE B 514 TYR 0.018 0.002 TYR B 289 ARG 0.004 0.001 ARG D 560 *********************** 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 351 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 325 time to evaluate : 1.631 Fit side-chains REVERT: A 149 MET cc_start: 0.8346 (mmm) cc_final: 0.7957 (mmm) REVERT: A 189 ASP cc_start: 0.8549 (t0) cc_final: 0.8325 (t70) REVERT: A 267 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8447 (mmm-85) REVERT: A 282 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 283 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7892 (tp30) REVERT: A 289 TYR cc_start: 0.8140 (m-80) cc_final: 0.7450 (t80) REVERT: A 317 PHE cc_start: 0.8254 (t80) cc_final: 0.8014 (t80) REVERT: A 433 ASP cc_start: 0.8120 (m-30) cc_final: 0.7902 (m-30) REVERT: A 445 ASP cc_start: 0.6836 (t0) cc_final: 0.6611 (t0) REVERT: A 515 ILE cc_start: 0.7713 (mt) cc_final: 0.7394 (tt) REVERT: A 517 HIS cc_start: 0.6228 (t70) cc_final: 0.5639 (t-90) REVERT: B 149 MET cc_start: 0.8359 (mmm) cc_final: 0.8117 (mmm) REVERT: B 265 LEU cc_start: 0.8346 (mt) cc_final: 0.8068 (mm) REVERT: B 283 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7962 (tp30) REVERT: B 289 TYR cc_start: 0.8139 (m-80) cc_final: 0.7472 (t80) REVERT: B 433 ASP cc_start: 0.8227 (m-30) cc_final: 0.8018 (m-30) REVERT: B 515 ILE cc_start: 0.7729 (mt) cc_final: 0.7389 (tt) REVERT: B 517 HIS cc_start: 0.6366 (t70) cc_final: 0.5776 (t-90) REVERT: C 149 MET cc_start: 0.8355 (mmm) cc_final: 0.8132 (mmm) REVERT: C 265 LEU cc_start: 0.8265 (mt) cc_final: 0.7987 (mm) REVERT: C 283 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7886 (tp30) REVERT: C 289 TYR cc_start: 0.8136 (m-80) cc_final: 0.7456 (t80) REVERT: C 433 ASP cc_start: 0.8157 (m-30) cc_final: 0.7946 (m-30) REVERT: C 515 ILE cc_start: 0.7798 (mt) cc_final: 0.7449 (tt) REVERT: C 517 HIS cc_start: 0.6194 (t70) cc_final: 0.5626 (t-90) REVERT: D 122 LYS cc_start: 0.9068 (tttt) cc_final: 0.8752 (tptp) REVERT: D 149 MET cc_start: 0.8349 (mmm) cc_final: 0.7974 (mmm) REVERT: D 189 ASP cc_start: 0.8570 (t0) cc_final: 0.8202 (t70) REVERT: D 192 MET cc_start: 0.8394 (mmm) cc_final: 0.8014 (mtp) REVERT: D 265 LEU cc_start: 0.8339 (mt) cc_final: 0.8064 (mm) REVERT: D 283 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7931 (tp30) REVERT: D 289 TYR cc_start: 0.8138 (m-80) cc_final: 0.7438 (t80) REVERT: D 317 PHE cc_start: 0.8267 (t80) cc_final: 0.8050 (t80) REVERT: D 433 ASP cc_start: 0.8118 (m-30) cc_final: 0.7898 (m-30) REVERT: D 445 ASP cc_start: 0.6778 (t0) cc_final: 0.6577 (t0) REVERT: D 515 ILE cc_start: 0.7777 (mt) cc_final: 0.7446 (tt) REVERT: D 517 HIS cc_start: 0.6168 (t70) cc_final: 0.5622 (t-90) outliers start: 26 outliers final: 16 residues processed: 343 average time/residue: 0.2143 time to fit residues: 114.1839 Evaluate side-chains 296 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 280 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 30.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN B 156 ASN B 568 ASN C 156 ASN C 300 ASN C 568 ASN D 156 ASN D 568 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14840 Z= 0.192 Angle : 0.505 6.050 20184 Z= 0.273 Chirality : 0.040 0.178 2268 Planarity : 0.004 0.043 2564 Dihedral : 3.960 16.938 2076 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.09 % Allowed : 9.40 % Favored : 88.51 % 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: 2.32 (0.20), residues: 1904 helix: 2.89 (0.14), residues: 1304 sheet: -1.98 (0.44), residues: 112 loop : -1.52 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 281 HIS 0.003 0.001 HIS A 392 PHE 0.016 0.001 PHE C 514 TYR 0.017 0.001 TYR D 289 ARG 0.007 0.000 ARG A 492 *********************** 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 373 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 345 time to evaluate : 1.638 Fit side-chains REVERT: A 149 MET cc_start: 0.8295 (mmm) cc_final: 0.8023 (mmm) REVERT: A 189 ASP cc_start: 0.8581 (t0) cc_final: 0.8379 (t70) REVERT: A 192 MET cc_start: 0.8429 (mmm) cc_final: 0.8222 (mtp) REVERT: A 283 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7932 (tp30) REVERT: A 289 TYR cc_start: 0.8157 (m-80) cc_final: 0.7491 (t80) REVERT: A 317 PHE cc_start: 0.8273 (t80) cc_final: 0.7974 (t80) REVERT: A 433 ASP cc_start: 0.8166 (m-30) cc_final: 0.7947 (m-30) REVERT: A 445 ASP cc_start: 0.6789 (t0) cc_final: 0.6552 (t0) REVERT: A 515 ILE cc_start: 0.7798 (mt) cc_final: 0.7483 (tt) REVERT: A 517 HIS cc_start: 0.5969 (t70) cc_final: 0.5570 (t-90) REVERT: B 149 MET cc_start: 0.8309 (mmm) cc_final: 0.7962 (mmm) REVERT: B 225 ASP cc_start: 0.7494 (m-30) cc_final: 0.7268 (m-30) REVERT: B 283 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7864 (tp30) REVERT: B 289 TYR cc_start: 0.8235 (m-80) cc_final: 0.7564 (t80) REVERT: B 433 ASP cc_start: 0.8078 (m-30) cc_final: 0.7865 (m-30) REVERT: B 445 ASP cc_start: 0.6790 (t0) cc_final: 0.6526 (t0) REVERT: B 452 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7907 (mt-10) REVERT: B 515 ILE cc_start: 0.7717 (mt) cc_final: 0.7386 (tt) REVERT: B 517 HIS cc_start: 0.6103 (t70) cc_final: 0.5692 (t-90) REVERT: C 149 MET cc_start: 0.8314 (mmm) cc_final: 0.7851 (mmm) REVERT: C 225 ASP cc_start: 0.7470 (m-30) cc_final: 0.7240 (m-30) REVERT: C 265 LEU cc_start: 0.8197 (mt) cc_final: 0.7994 (mm) REVERT: C 283 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7890 (tp30) REVERT: C 289 TYR cc_start: 0.8214 (m-80) cc_final: 0.7562 (t80) REVERT: C 433 ASP cc_start: 0.8156 (m-30) cc_final: 0.7936 (m-30) REVERT: C 445 ASP cc_start: 0.6932 (t0) cc_final: 0.6700 (t0) REVERT: C 515 ILE cc_start: 0.7832 (mt) cc_final: 0.7564 (tt) REVERT: C 517 HIS cc_start: 0.5934 (t70) cc_final: 0.5468 (t-90) REVERT: D 122 LYS cc_start: 0.9071 (tttt) cc_final: 0.8754 (tptp) REVERT: D 149 MET cc_start: 0.8340 (mmm) cc_final: 0.7981 (mmm) REVERT: D 192 MET cc_start: 0.8434 (mmm) cc_final: 0.8231 (mtp) REVERT: D 265 LEU cc_start: 0.8218 (mt) cc_final: 0.7975 (mm) REVERT: D 283 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7932 (tp30) REVERT: D 289 TYR cc_start: 0.8174 (m-80) cc_final: 0.7445 (t80) REVERT: D 317 PHE cc_start: 0.8304 (t80) cc_final: 0.8035 (t80) REVERT: D 433 ASP cc_start: 0.8161 (m-30) cc_final: 0.7939 (m-30) REVERT: D 445 ASP cc_start: 0.6789 (t0) cc_final: 0.6561 (t0) REVERT: D 515 ILE cc_start: 0.7800 (mt) cc_final: 0.7558 (tt) REVERT: D 517 HIS cc_start: 0.5926 (t70) cc_final: 0.5458 (t-90) outliers start: 28 outliers final: 17 residues processed: 363 average time/residue: 0.2077 time to fit residues: 117.0901 Evaluate side-chains 326 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 309 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 175 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 91 optimal weight: 0.0270 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- 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 517 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS ** C 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14840 Z= 0.155 Angle : 0.479 7.450 20184 Z= 0.257 Chirality : 0.039 0.179 2268 Planarity : 0.003 0.037 2564 Dihedral : 3.822 15.380 2076 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.31 % Allowed : 12.54 % Favored : 85.15 % 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: 2.71 (0.14), residues: 1308 sheet: -1.84 (0.43), residues: 120 loop : -1.27 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 330 HIS 0.002 0.001 HIS B 437 PHE 0.014 0.001 PHE C 514 TYR 0.013 0.001 TYR B 144 ARG 0.007 0.000 ARG A 492 *********************** 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 363 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 332 time to evaluate : 1.627 Fit side-chains REVERT: A 149 MET cc_start: 0.8293 (mmm) cc_final: 0.7932 (mmm) REVERT: A 265 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7536 (mm) REVERT: A 282 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7781 (mt-10) REVERT: A 283 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7891 (tp30) REVERT: A 289 TYR cc_start: 0.8261 (m-80) cc_final: 0.7451 (t80) REVERT: A 317 PHE cc_start: 0.8350 (t80) cc_final: 0.8054 (t80) REVERT: A 433 ASP cc_start: 0.8159 (m-30) cc_final: 0.7931 (m-30) REVERT: A 445 ASP cc_start: 0.6866 (t0) cc_final: 0.6626 (t0) REVERT: A 517 HIS cc_start: 0.6158 (t-90) cc_final: 0.5827 (t-90) REVERT: B 225 ASP cc_start: 0.7477 (m-30) cc_final: 0.7186 (m-30) REVERT: B 283 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7922 (tp30) REVERT: B 289 TYR cc_start: 0.8268 (m-80) cc_final: 0.7459 (t80) REVERT: B 433 ASP cc_start: 0.8164 (m-30) cc_final: 0.7934 (m-30) REVERT: B 445 ASP cc_start: 0.6848 (t0) cc_final: 0.6595 (t0) REVERT: B 515 ILE cc_start: 0.7555 (mt) cc_final: 0.7349 (tt) REVERT: B 517 HIS cc_start: 0.5882 (t70) cc_final: 0.5470 (t-90) REVERT: C 225 ASP cc_start: 0.7449 (m-30) cc_final: 0.7159 (m-30) REVERT: C 283 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7917 (tp30) REVERT: C 289 TYR cc_start: 0.8259 (m-80) cc_final: 0.7446 (t80) REVERT: C 433 ASP cc_start: 0.8151 (m-30) cc_final: 0.7934 (m-30) REVERT: C 445 ASP cc_start: 0.6904 (t0) cc_final: 0.6682 (t0) REVERT: C 515 ILE cc_start: 0.7683 (mt) cc_final: 0.7445 (tt) REVERT: C 517 HIS cc_start: 0.5789 (t70) cc_final: 0.5458 (t-90) REVERT: D 122 LYS cc_start: 0.9060 (tttt) cc_final: 0.8770 (tptp) REVERT: D 125 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8651 (mm-30) REVERT: D 149 MET cc_start: 0.8240 (mmm) cc_final: 0.7924 (tpp) REVERT: D 283 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7945 (tp30) REVERT: D 289 TYR cc_start: 0.8260 (m-80) cc_final: 0.7449 (t80) REVERT: D 317 PHE cc_start: 0.8305 (t80) cc_final: 0.8024 (t80) REVERT: D 433 ASP cc_start: 0.8155 (m-30) cc_final: 0.7928 (m-30) REVERT: D 445 ASP cc_start: 0.6791 (t0) cc_final: 0.6539 (t0) REVERT: D 515 ILE cc_start: 0.7657 (mt) cc_final: 0.7411 (tt) REVERT: D 517 HIS cc_start: 0.5783 (t70) cc_final: 0.5420 (t-90) outliers start: 31 outliers final: 17 residues processed: 348 average time/residue: 0.2052 time to fit residues: 111.3839 Evaluate side-chains 304 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 286 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.0870 chunk 105 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3229 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= 0.187 Angle : 0.482 8.025 20184 Z= 0.260 Chirality : 0.039 0.199 2268 Planarity : 0.003 0.040 2564 Dihedral : 3.786 16.535 2076 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.46 % Allowed : 14.10 % Favored : 83.43 % 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: 2.20 (0.19), residues: 1904 helix: 2.60 (0.14), residues: 1312 sheet: -1.59 (0.43), residues: 120 loop : -1.11 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 145 HIS 0.003 0.001 HIS C 392 PHE 0.016 0.001 PHE B 514 TYR 0.012 0.001 TYR C 144 ARG 0.007 0.000 ARG A 492 *********************** 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 330 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 297 time to evaluate : 1.891 Fit side-chains REVERT: A 265 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7466 (mm) REVERT: A 283 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7952 (tp30) REVERT: A 289 TYR cc_start: 0.8265 (m-80) cc_final: 0.7444 (t80) REVERT: A 317 PHE cc_start: 0.8190 (t80) cc_final: 0.7880 (t80) REVERT: A 369 MET cc_start: 0.7241 (mmm) cc_final: 0.6803 (mmm) REVERT: A 433 ASP cc_start: 0.8152 (m-30) cc_final: 0.7936 (m-30) REVERT: A 445 ASP cc_start: 0.6892 (t0) cc_final: 0.6666 (t0) REVERT: A 517 HIS cc_start: 0.5963 (t-90) cc_final: 0.5705 (t-90) REVERT: B 149 MET cc_start: 0.8633 (mmm) cc_final: 0.8256 (tpp) REVERT: B 225 ASP cc_start: 0.7466 (m-30) cc_final: 0.7150 (m-30) REVERT: B 283 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7927 (tp30) REVERT: B 369 MET cc_start: 0.7239 (mmm) cc_final: 0.6806 (mmm) REVERT: B 433 ASP cc_start: 0.8066 (m-30) cc_final: 0.7854 (m-30) REVERT: B 445 ASP cc_start: 0.6886 (t0) cc_final: 0.6661 (t0) REVERT: B 517 HIS cc_start: 0.5856 (t70) cc_final: 0.5452 (t-90) REVERT: C 225 ASP cc_start: 0.7421 (m-30) cc_final: 0.7096 (m-30) REVERT: C 283 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7945 (tp30) REVERT: C 369 MET cc_start: 0.7090 (mmm) cc_final: 0.6652 (mmm) REVERT: C 433 ASP cc_start: 0.8145 (m-30) cc_final: 0.7930 (m-30) REVERT: C 445 ASP cc_start: 0.6958 (t0) cc_final: 0.6730 (t0) REVERT: C 515 ILE cc_start: 0.7662 (mt) cc_final: 0.7451 (tt) REVERT: C 517 HIS cc_start: 0.6327 (t-90) cc_final: 0.5991 (t-90) REVERT: D 122 LYS cc_start: 0.9099 (tttt) cc_final: 0.8829 (tptp) REVERT: D 125 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8850 (mm-30) REVERT: D 149 MET cc_start: 0.8123 (mmm) cc_final: 0.7812 (tpp) REVERT: D 265 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7699 (mm) REVERT: D 282 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7614 (mt-10) REVERT: D 283 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7951 (tp30) REVERT: D 289 TYR cc_start: 0.8269 (m-80) cc_final: 0.7446 (t80) REVERT: D 317 PHE cc_start: 0.8309 (t80) cc_final: 0.8020 (t80) REVERT: D 369 MET cc_start: 0.7225 (mmm) cc_final: 0.6788 (mmm) REVERT: D 433 ASP cc_start: 0.8147 (m-30) cc_final: 0.7932 (m-30) REVERT: D 445 ASP cc_start: 0.6894 (t0) cc_final: 0.6662 (t0) REVERT: D 515 ILE cc_start: 0.7635 (mt) cc_final: 0.7419 (tt) REVERT: D 517 HIS cc_start: 0.5828 (t70) cc_final: 0.5385 (t-90) outliers start: 33 outliers final: 21 residues processed: 315 average time/residue: 0.2054 time to fit residues: 102.6112 Evaluate side-chains 304 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 281 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 8.9990 chunk 167 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** B 517 HIS ** 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: 0.6567 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14840 Z= 0.165 Angle : 0.478 7.348 20184 Z= 0.255 Chirality : 0.039 0.280 2268 Planarity : 0.003 0.034 2564 Dihedral : 3.762 17.466 2076 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.39 % Allowed : 15.90 % 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: 2.22 (0.19), residues: 1904 helix: 2.55 (0.14), residues: 1312 sheet: -1.32 (0.44), residues: 120 loop : -0.96 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 281 HIS 0.002 0.001 HIS C 421 PHE 0.020 0.001 PHE A 514 TYR 0.009 0.001 TYR C 411 ARG 0.008 0.000 ARG A 492 *********************** 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 325 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 293 time to evaluate : 1.724 Fit side-chains REVERT: A 149 MET cc_start: 0.8385 (tpp) cc_final: 0.8170 (tpp) REVERT: A 265 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7406 (mm) REVERT: A 283 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7954 (tp30) REVERT: A 317 PHE cc_start: 0.8210 (t80) cc_final: 0.7935 (t80) REVERT: A 433 ASP cc_start: 0.8142 (m-30) cc_final: 0.7930 (m-30) REVERT: A 445 ASP cc_start: 0.6889 (t0) cc_final: 0.6657 (t0) REVERT: A 517 HIS cc_start: 0.5964 (t-90) cc_final: 0.5731 (t-90) REVERT: B 140 ASP cc_start: 0.7381 (t70) cc_final: 0.7085 (t70) REVERT: B 149 MET cc_start: 0.8658 (mmm) cc_final: 0.8389 (tpp) REVERT: B 225 ASP cc_start: 0.7461 (m-30) cc_final: 0.7131 (m-30) REVERT: B 265 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7332 (mm) REVERT: B 283 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7946 (tp30) REVERT: B 433 ASP cc_start: 0.8147 (m-30) cc_final: 0.7931 (m-30) REVERT: B 445 ASP cc_start: 0.6884 (t0) cc_final: 0.6653 (t0) REVERT: B 517 HIS cc_start: 0.5625 (t70) cc_final: 0.5289 (t-90) REVERT: C 225 ASP cc_start: 0.7415 (m-30) cc_final: 0.7080 (m-30) REVERT: C 433 ASP cc_start: 0.8135 (m-30) cc_final: 0.7925 (m-30) REVERT: C 445 ASP cc_start: 0.6904 (t0) cc_final: 0.6672 (t0) REVERT: C 515 ILE cc_start: 0.7622 (mt) cc_final: 0.7407 (tt) REVERT: C 517 HIS cc_start: 0.6030 (t-90) cc_final: 0.5736 (t-90) REVERT: D 122 LYS cc_start: 0.9037 (tttt) cc_final: 0.8786 (tptp) REVERT: D 149 MET cc_start: 0.8014 (mmm) cc_final: 0.7698 (tpp) REVERT: D 265 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7554 (mm) REVERT: D 282 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7564 (mt-10) REVERT: D 283 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7954 (tp30) REVERT: D 289 TYR cc_start: 0.8260 (m-80) cc_final: 0.7434 (t80) REVERT: D 317 PHE cc_start: 0.8261 (t80) cc_final: 0.7985 (t80) REVERT: D 433 ASP cc_start: 0.8142 (m-30) cc_final: 0.7931 (m-30) REVERT: D 445 ASP cc_start: 0.6893 (t0) cc_final: 0.6658 (t0) REVERT: D 515 ILE cc_start: 0.7656 (mt) cc_final: 0.7454 (tt) REVERT: D 517 HIS cc_start: 0.5892 (t70) cc_final: 0.5423 (t-90) outliers start: 32 outliers final: 21 residues processed: 309 average time/residue: 0.2022 time to fit residues: 99.7024 Evaluate side-chains 302 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 278 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.6563 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14840 Z= 0.164 Angle : 0.494 8.917 20184 Z= 0.264 Chirality : 0.039 0.307 2268 Planarity : 0.003 0.033 2564 Dihedral : 3.739 18.271 2076 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.09 % Allowed : 17.01 % 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: 2.23 (0.19), residues: 1904 helix: 2.50 (0.14), residues: 1316 sheet: -1.10 (0.45), residues: 120 loop : -0.85 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 145 HIS 0.002 0.001 HIS B 437 PHE 0.020 0.001 PHE B 514 TYR 0.016 0.001 TYR B 144 ARG 0.007 0.000 ARG A 492 *********************** 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 319 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 291 time to evaluate : 1.791 Fit side-chains REVERT: A 149 MET cc_start: 0.8336 (tpp) cc_final: 0.7949 (tpp) REVERT: A 265 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7463 (mm) REVERT: A 317 PHE cc_start: 0.8182 (t80) cc_final: 0.7907 (t80) REVERT: A 369 MET cc_start: 0.7334 (mmm) cc_final: 0.6931 (ptt) REVERT: A 433 ASP cc_start: 0.8141 (m-30) cc_final: 0.7930 (m-30) REVERT: A 445 ASP cc_start: 0.6945 (t0) cc_final: 0.6694 (t0) REVERT: A 512 MET cc_start: 0.8024 (tmm) cc_final: 0.7775 (tmm) REVERT: A 517 HIS cc_start: 0.5954 (t-90) cc_final: 0.5735 (t-90) REVERT: B 149 MET cc_start: 0.8663 (mmm) cc_final: 0.8344 (tpp) REVERT: B 225 ASP cc_start: 0.7465 (m-30) cc_final: 0.7120 (m-30) REVERT: B 283 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7951 (tp30) REVERT: B 369 MET cc_start: 0.7343 (mmm) cc_final: 0.6936 (ptt) REVERT: B 406 GLN cc_start: 0.7943 (mt0) cc_final: 0.7733 (mt0) REVERT: B 433 ASP cc_start: 0.8145 (m-30) cc_final: 0.7930 (m-30) REVERT: B 445 ASP cc_start: 0.6880 (t0) cc_final: 0.6645 (t0) REVERT: B 512 MET cc_start: 0.8056 (tmm) cc_final: 0.7795 (tmm) REVERT: B 517 HIS cc_start: 0.5628 (t70) cc_final: 0.5305 (t-90) REVERT: C 149 MET cc_start: 0.8256 (tpp) cc_final: 0.7994 (mpp) REVERT: C 225 ASP cc_start: 0.7494 (m-30) cc_final: 0.7146 (m-30) REVERT: C 265 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7422 (mm) REVERT: C 369 MET cc_start: 0.7344 (mmm) cc_final: 0.6970 (ptt) REVERT: C 433 ASP cc_start: 0.8136 (m-30) cc_final: 0.7925 (m-30) REVERT: C 445 ASP cc_start: 0.6899 (t0) cc_final: 0.6664 (t0) REVERT: C 512 MET cc_start: 0.8039 (tmm) cc_final: 0.7794 (tmm) REVERT: C 515 ILE cc_start: 0.7582 (mt) cc_final: 0.7373 (tt) REVERT: C 517 HIS cc_start: 0.6120 (t-90) cc_final: 0.5814 (t-90) REVERT: D 122 LYS cc_start: 0.9054 (tttt) cc_final: 0.8767 (tptp) REVERT: D 149 MET cc_start: 0.7990 (mmm) cc_final: 0.7738 (tpp) REVERT: D 265 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7564 (mm) REVERT: D 282 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7631 (mt-10) REVERT: D 283 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7980 (tp30) REVERT: D 317 PHE cc_start: 0.8252 (t80) cc_final: 0.7986 (t80) REVERT: D 369 MET cc_start: 0.7318 (mmm) cc_final: 0.6951 (ptt) REVERT: D 433 ASP cc_start: 0.8141 (m-30) cc_final: 0.7922 (m-30) REVERT: D 445 ASP cc_start: 0.6889 (t0) cc_final: 0.6651 (t0) REVERT: D 494 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7309 (mt-10) REVERT: D 512 MET cc_start: 0.7934 (tmm) cc_final: 0.7700 (tmm) REVERT: D 517 HIS cc_start: 0.5935 (t70) cc_final: 0.5435 (t-90) outliers start: 28 outliers final: 22 residues processed: 307 average time/residue: 0.2131 time to fit residues: 105.9536 Evaluate side-chains 306 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 281 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.0170 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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** B 286 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14840 Z= 0.141 Angle : 0.485 8.447 20184 Z= 0.256 Chirality : 0.039 0.389 2268 Planarity : 0.003 0.037 2564 Dihedral : 3.677 17.597 2076 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.87 % Allowed : 16.64 % 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: 2.29 (0.19), residues: 1904 helix: 2.50 (0.14), residues: 1316 sheet: -0.93 (0.45), residues: 120 loop : -0.73 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 145 HIS 0.002 0.001 HIS C 286 PHE 0.028 0.001 PHE A 514 TYR 0.008 0.001 TYR C 411 ARG 0.008 0.000 ARG A 492 *********************** 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 320 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 295 time to evaluate : 1.900 Fit side-chains REVERT: A 149 MET cc_start: 0.8303 (tpp) cc_final: 0.8032 (tpp) REVERT: A 265 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7297 (mm) REVERT: A 317 PHE cc_start: 0.8164 (t80) cc_final: 0.7902 (t80) REVERT: A 369 MET cc_start: 0.7252 (mmm) cc_final: 0.6831 (ptt) REVERT: A 433 ASP cc_start: 0.8140 (m-30) cc_final: 0.7920 (m-30) REVERT: A 445 ASP cc_start: 0.6934 (t0) cc_final: 0.6678 (t0) REVERT: A 517 HIS cc_start: 0.5937 (t-90) cc_final: 0.5725 (t-90) REVERT: B 149 MET cc_start: 0.8670 (mmm) cc_final: 0.8332 (tpp) REVERT: B 225 ASP cc_start: 0.7398 (m-30) cc_final: 0.7023 (m-30) REVERT: B 283 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7985 (tp30) REVERT: B 369 MET cc_start: 0.7146 (mmm) cc_final: 0.6712 (ptt) REVERT: B 433 ASP cc_start: 0.8144 (m-30) cc_final: 0.7930 (m-30) REVERT: B 445 ASP cc_start: 0.6872 (t0) cc_final: 0.6633 (t0) REVERT: B 517 HIS cc_start: 0.5623 (t70) cc_final: 0.5307 (t-90) REVERT: C 225 ASP cc_start: 0.7420 (m-30) cc_final: 0.7048 (m-30) REVERT: C 265 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7378 (mm) REVERT: C 369 MET cc_start: 0.7259 (mmm) cc_final: 0.6839 (ptt) REVERT: C 433 ASP cc_start: 0.8135 (m-30) cc_final: 0.7925 (m-30) REVERT: C 445 ASP cc_start: 0.6891 (t0) cc_final: 0.6650 (t0) REVERT: C 512 MET cc_start: 0.8027 (tmm) cc_final: 0.7795 (tmm) REVERT: C 515 ILE cc_start: 0.7593 (mt) cc_final: 0.7390 (tt) REVERT: C 517 HIS cc_start: 0.6017 (t-90) cc_final: 0.5710 (t-90) REVERT: D 122 LYS cc_start: 0.9023 (tttt) cc_final: 0.8762 (tptp) REVERT: D 149 MET cc_start: 0.7969 (mmm) cc_final: 0.7687 (tpp) REVERT: D 265 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7492 (mm) REVERT: D 283 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7996 (tp30) REVERT: D 317 PHE cc_start: 0.8219 (t80) cc_final: 0.7899 (t80) REVERT: D 369 MET cc_start: 0.7338 (mmm) cc_final: 0.6924 (ptt) REVERT: D 433 ASP cc_start: 0.8141 (m-30) cc_final: 0.7923 (m-30) REVERT: D 445 ASP cc_start: 0.6940 (t0) cc_final: 0.6682 (t0) REVERT: D 517 HIS cc_start: 0.5895 (t70) cc_final: 0.5402 (t-90) outliers start: 25 outliers final: 18 residues processed: 308 average time/residue: 0.1968 time to fit residues: 97.3290 Evaluate side-chains 303 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 282 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.0570 chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 0.3980 chunk 163 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14840 Z= 0.147 Angle : 0.496 7.731 20184 Z= 0.263 Chirality : 0.039 0.378 2268 Planarity : 0.003 0.034 2564 Dihedral : 3.648 17.942 2076 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.94 % Allowed : 17.46 % Favored : 80.60 % 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: 2.34 (0.19), residues: 1904 helix: 2.51 (0.14), residues: 1316 sheet: -0.82 (0.45), residues: 120 loop : -0.61 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 145 HIS 0.002 0.001 HIS B 437 PHE 0.031 0.001 PHE A 514 TYR 0.008 0.001 TYR B 407 ARG 0.008 0.000 ARG A 492 *********************** 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 317 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 291 time to evaluate : 1.581 Fit side-chains REVERT: A 145 TRP cc_start: 0.8044 (t-100) cc_final: 0.7664 (t-100) REVERT: A 149 MET cc_start: 0.8399 (tpp) cc_final: 0.8050 (tpp) REVERT: A 265 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7362 (mm) REVERT: A 433 ASP cc_start: 0.8141 (m-30) cc_final: 0.7922 (m-30) REVERT: A 445 ASP cc_start: 0.6925 (t0) cc_final: 0.6667 (t0) REVERT: A 512 MET cc_start: 0.8046 (tmm) cc_final: 0.7791 (tmm) REVERT: A 517 HIS cc_start: 0.5935 (t-90) cc_final: 0.5729 (t-90) REVERT: B 149 MET cc_start: 0.8677 (mmm) cc_final: 0.8333 (tpp) REVERT: B 225 ASP cc_start: 0.7435 (m-30) cc_final: 0.7058 (m-30) REVERT: B 283 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7984 (tp30) REVERT: B 369 MET cc_start: 0.7145 (mmm) cc_final: 0.6727 (ptt) REVERT: B 433 ASP cc_start: 0.8144 (m-30) cc_final: 0.7930 (m-30) REVERT: B 445 ASP cc_start: 0.6925 (t0) cc_final: 0.6656 (t0) REVERT: B 512 MET cc_start: 0.8019 (tmm) cc_final: 0.7783 (tmm) REVERT: B 517 HIS cc_start: 0.5620 (t70) cc_final: 0.5307 (t-90) REVERT: C 145 TRP cc_start: 0.8028 (t-100) cc_final: 0.7308 (t-100) REVERT: C 225 ASP cc_start: 0.7465 (m-30) cc_final: 0.7090 (m-30) REVERT: C 265 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7418 (mm) REVERT: C 369 MET cc_start: 0.7131 (mmm) cc_final: 0.6711 (ptt) REVERT: C 433 ASP cc_start: 0.8137 (m-30) cc_final: 0.7927 (m-30) REVERT: C 445 ASP cc_start: 0.6886 (t0) cc_final: 0.6643 (t0) REVERT: C 515 ILE cc_start: 0.7573 (mt) cc_final: 0.7331 (mp) REVERT: C 517 HIS cc_start: 0.5838 (t-90) cc_final: 0.5560 (t-90) REVERT: D 122 LYS cc_start: 0.9012 (tttt) cc_final: 0.8743 (tptp) REVERT: D 149 MET cc_start: 0.7955 (mmm) cc_final: 0.7674 (tpp) REVERT: D 265 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7634 (mm) REVERT: D 283 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7998 (tp30) REVERT: D 369 MET cc_start: 0.7248 (mmm) cc_final: 0.6818 (ptt) REVERT: D 433 ASP cc_start: 0.8144 (m-30) cc_final: 0.7926 (m-30) REVERT: D 445 ASP cc_start: 0.6934 (t0) cc_final: 0.6679 (t0) REVERT: D 512 MET cc_start: 0.8021 (tmm) cc_final: 0.7788 (tmm) REVERT: D 517 HIS cc_start: 0.5915 (t70) cc_final: 0.5432 (t-90) outliers start: 26 outliers final: 21 residues processed: 306 average time/residue: 0.1940 time to fit residues: 95.3115 Evaluate side-chains 314 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 290 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14840 Z= 0.247 Angle : 0.527 10.733 20184 Z= 0.282 Chirality : 0.041 0.388 2268 Planarity : 0.003 0.034 2564 Dihedral : 3.707 17.601 2076 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.46 % Allowed : 16.72 % Favored : 80.82 % 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: 2.29 (0.19), residues: 1904 helix: 2.43 (0.14), residues: 1340 sheet: -0.78 (0.45), residues: 120 loop : -0.70 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 281 HIS 0.004 0.001 HIS D 392 PHE 0.029 0.001 PHE A 514 TYR 0.007 0.001 TYR D 347 ARG 0.009 0.000 ARG B 492 ********************** 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 323 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 290 time to evaluate : 1.686 Fit side-chains REVERT: A 145 TRP cc_start: 0.8023 (t-100) cc_final: 0.7631 (t-100) REVERT: A 149 MET cc_start: 0.8415 (tpp) cc_final: 0.8041 (tpp) REVERT: A 265 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7406 (mm) REVERT: A 317 PHE cc_start: 0.8081 (t80) cc_final: 0.7873 (t80) REVERT: A 369 MET cc_start: 0.7227 (mmm) cc_final: 0.6814 (ptt) REVERT: A 433 ASP cc_start: 0.8142 (m-30) cc_final: 0.7933 (m-30) REVERT: A 445 ASP cc_start: 0.6931 (t0) cc_final: 0.6673 (t0) REVERT: A 512 MET cc_start: 0.8051 (tmm) cc_final: 0.7811 (tmm) REVERT: A 517 HIS cc_start: 0.5996 (t-90) cc_final: 0.5790 (t-90) REVERT: B 149 MET cc_start: 0.8654 (mmm) cc_final: 0.8292 (tpp) REVERT: B 225 ASP cc_start: 0.7548 (m-30) cc_final: 0.7195 (m-30) REVERT: B 283 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7992 (tp30) REVERT: B 317 PHE cc_start: 0.8073 (t80) cc_final: 0.7845 (t80) REVERT: B 433 ASP cc_start: 0.8055 (m-30) cc_final: 0.7848 (m-30) REVERT: B 445 ASP cc_start: 0.6927 (t0) cc_final: 0.6671 (t0) REVERT: B 512 MET cc_start: 0.8021 (tmm) cc_final: 0.7784 (tmm) REVERT: B 517 HIS cc_start: 0.5675 (t70) cc_final: 0.5360 (t-90) REVERT: C 145 TRP cc_start: 0.8192 (t-100) cc_final: 0.7707 (t-100) REVERT: C 149 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7886 (mpp) REVERT: C 225 ASP cc_start: 0.7464 (m-30) cc_final: 0.7093 (m-30) REVERT: C 265 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7481 (mm) REVERT: C 433 ASP cc_start: 0.8046 (m-30) cc_final: 0.7846 (m-30) REVERT: C 445 ASP cc_start: 0.6886 (t0) cc_final: 0.6644 (t0) REVERT: C 512 MET cc_start: 0.8007 (tmm) cc_final: 0.7783 (tmm) REVERT: C 517 HIS cc_start: 0.5773 (t-90) cc_final: 0.5473 (t-90) REVERT: D 122 LYS cc_start: 0.9012 (tttt) cc_final: 0.8740 (tptp) REVERT: D 149 MET cc_start: 0.8024 (mmm) cc_final: 0.7733 (tpp) REVERT: D 265 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7538 (mm) REVERT: D 282 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7624 (mt-10) REVERT: D 283 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7992 (tp30) REVERT: D 433 ASP cc_start: 0.8144 (m-30) cc_final: 0.7928 (m-30) REVERT: D 445 ASP cc_start: 0.6939 (t0) cc_final: 0.6682 (t0) REVERT: D 512 MET cc_start: 0.8015 (tmm) cc_final: 0.7783 (tmm) REVERT: D 517 HIS cc_start: 0.5931 (t70) cc_final: 0.5442 (t-90) outliers start: 33 outliers final: 26 residues processed: 306 average time/residue: 0.1941 time to fit residues: 95.2425 Evaluate side-chains 316 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 286 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 140 optimal weight: 20.0000 chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 0.0370 chunk 156 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 133 optimal weight: 0.0470 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091423 restraints weight = 34477.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.091531 restraints weight = 16673.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092275 restraints weight = 13655.874| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14840 Z= 0.145 Angle : 0.511 10.370 20184 Z= 0.272 Chirality : 0.040 0.383 2268 Planarity : 0.003 0.036 2564 Dihedral : 3.699 20.894 2076 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.87 % Allowed : 17.99 % Favored : 80.15 % 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: 2.31 (0.19), residues: 1904 helix: 2.47 (0.14), residues: 1328 sheet: -0.65 (0.45), residues: 120 loop : -0.73 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 145 HIS 0.002 0.001 HIS A 437 PHE 0.033 0.001 PHE D 317 TYR 0.008 0.001 TYR B 407 ARG 0.009 0.000 ARG A 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2853.57 seconds wall clock time: 52 minutes 24.98 seconds (3144.98 seconds total)