Starting phenix.real_space_refine (version: dev) on Tue Feb 21 20:37:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2023/5u6p_8512_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2023/5u6p_8512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2023/5u6p_8512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2023/5u6p_8512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2023/5u6p_8512_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2023/5u6p_8512_updated.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "A PHE 178": "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 TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "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 TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "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 TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 178": "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 TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15640 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3793 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain breaks: 2 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3793 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain breaks: 2 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3793 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain breaks: 2 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3793 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain breaks: 2 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "H" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 8.96, per 1000 atoms: 0.57 Number of scatterers: 15640 At special positions: 0 Unit cell: (123.5, 123.5, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 4 15.00 O 2676 8.00 N 2688 7.00 C 10156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.57 Conformation dependent library (CDL) restraints added in 2.3 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 8 sheets defined 70.6% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.722A pdb=" N THR A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.934A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 253 through 289 removed outlier: 3.810A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 322 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.518A pdb=" N ASN A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 334' Processing helix chain 'A' and resid 341 through 357 Processing helix chain 'A' and resid 369 through 400 Processing helix chain 'A' and resid 402 through 421 removed outlier: 3.674A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 439 Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.570A pdb=" N ASN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 465 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.890A pdb=" N ASN A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 478' Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.661A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 566 through 575 removed outlier: 3.678A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 removed outlier: 3.780A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.722A pdb=" N THR B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 166 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 173 through 195 removed outlier: 3.935A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 253 through 289 removed outlier: 3.811A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N SER B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 322 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.519A pdb=" N ASN B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'B' and resid 341 through 357 Processing helix chain 'B' and resid 369 through 400 Processing helix chain 'B' and resid 402 through 421 removed outlier: 3.675A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 439 Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.572A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 465 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.891A pdb=" N ASN B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 474 through 478' Processing helix chain 'B' and resid 481 through 490 removed outlier: 3.663A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 566 through 575 removed outlier: 3.678A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 594 removed outlier: 3.779A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'F' and resid 3 through 18 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.723A pdb=" N THR C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 166 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 173 through 195 removed outlier: 3.935A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 253 through 289 removed outlier: 3.810A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU C 271 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N SER C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 322 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.519A pdb=" N ASN C 334 " --> pdb=" O TRP C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 334' Processing helix chain 'C' and resid 341 through 357 Processing helix chain 'C' and resid 369 through 400 Processing helix chain 'C' and resid 402 through 421 removed outlier: 3.676A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 439 Processing helix chain 'C' and resid 446 through 452 removed outlier: 3.571A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.890A pdb=" N ASN C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 474 through 478' Processing helix chain 'C' and resid 481 through 490 removed outlier: 3.662A pdb=" N LYS C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 545 Processing helix chain 'C' and resid 566 through 575 removed outlier: 3.679A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 594 removed outlier: 3.780A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'G' and resid 3 through 18 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.722A pdb=" N THR D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 166 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 173 through 195 removed outlier: 3.935A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 232 through 241 Processing helix chain 'D' and resid 253 through 289 removed outlier: 3.811A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N SER D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 322 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.518A pdb=" N ASN D 334 " --> pdb=" O TRP D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 330 through 334' Processing helix chain 'D' and resid 341 through 357 Processing helix chain 'D' and resid 369 through 400 Processing helix chain 'D' and resid 402 through 421 removed outlier: 3.679A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 439 Processing helix chain 'D' and resid 446 through 452 removed outlier: 3.571A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 465 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.890A pdb=" N ASN D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 478' Processing helix chain 'D' and resid 481 through 490 removed outlier: 3.662A pdb=" N LYS D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 545 Processing helix chain 'D' and resid 566 through 575 removed outlier: 3.677A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 594 removed outlier: 3.779A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 607 Processing helix chain 'H' and resid 3 through 18 Processing sheet with id= A, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.688A pdb=" N TYR A 562 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE A 515 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 564 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR A 513 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 530 through 532 removed outlier: 3.761A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.690A pdb=" N TYR B 562 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE B 515 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 564 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR B 513 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 530 through 532 removed outlier: 3.761A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.689A pdb=" N TYR C 562 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE C 515 " --> pdb=" O TYR C 562 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU C 564 " --> pdb=" O TYR C 513 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR C 513 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 530 through 532 removed outlier: 3.761A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.688A pdb=" N TYR D 562 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE D 515 " --> pdb=" O TYR D 562 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU D 564 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR D 513 " --> pdb=" O LEU D 564 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.762A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2892 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: 4.97 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4708 1.34 - 1.46: 2376 1.46 - 1.57: 8720 1.57 - 1.69: 8 1.69 - 1.81: 204 Bond restraints: 16016 Sorted by residual: bond pdb=" CA ILE C 160 " pdb=" CB ILE C 160 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.35e+01 bond pdb=" CA ILE B 160 " pdb=" CB ILE B 160 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.34e+01 bond pdb=" CA ILE D 160 " pdb=" CB ILE D 160 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.27e+01 bond pdb=" CA ILE A 160 " pdb=" CB ILE A 160 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.19e+01 bond pdb=" C SER C 346 " pdb=" O SER C 346 " ideal model delta sigma weight residual 1.236 1.275 -0.039 1.15e-02 7.56e+03 1.15e+01 ... (remaining 16011 not shown) Histogram of bond angle deviations from ideal: 95.86 - 103.93: 207 103.93 - 111.99: 7058 111.99 - 120.05: 6969 120.05 - 128.12: 7430 128.12 - 136.18: 136 Bond angle restraints: 21800 Sorted by residual: angle pdb=" O ILE D 160 " pdb=" C ILE D 160 " pdb=" N PRO D 161 " ideal model delta sigma weight residual 120.42 124.84 -4.42 6.40e-01 2.44e+00 4.77e+01 angle pdb=" O ILE A 160 " pdb=" C ILE A 160 " pdb=" N PRO A 161 " ideal model delta sigma weight residual 120.42 124.81 -4.39 6.40e-01 2.44e+00 4.70e+01 angle pdb=" O ILE C 160 " pdb=" C ILE C 160 " pdb=" N PRO C 161 " ideal model delta sigma weight residual 120.42 124.79 -4.37 6.40e-01 2.44e+00 4.66e+01 angle pdb=" O ILE B 160 " pdb=" C ILE B 160 " pdb=" N PRO B 161 " ideal model delta sigma weight residual 120.42 124.79 -4.37 6.40e-01 2.44e+00 4.66e+01 angle pdb=" O THR D 173 " pdb=" C THR D 173 " pdb=" N PRO D 174 " ideal model delta sigma weight residual 120.38 125.11 -4.73 7.90e-01 1.60e+00 3.59e+01 ... (remaining 21795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 9304 31.61 - 63.21: 64 63.21 - 94.82: 0 94.82 - 126.43: 0 126.43 - 158.03: 12 Dihedral angle restraints: 9380 sinusoidal: 3224 harmonic: 6156 Sorted by residual: dihedral pdb=" C5' CMP D 901 " pdb=" O5' CMP D 901 " pdb=" P CMP D 901 " pdb=" O1P CMP D 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.97 -158.03 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' CMP C 901 " pdb=" O5' CMP C 901 " pdb=" P CMP C 901 " pdb=" O1P CMP C 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.98 -158.02 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' CMP B 901 " pdb=" O5' CMP B 901 " pdb=" P CMP B 901 " pdb=" O1P CMP B 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.99 -158.01 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1587 0.057 - 0.114: 591 0.114 - 0.171: 229 0.171 - 0.228: 51 0.228 - 0.285: 26 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CA HIS D 279 " pdb=" N HIS D 279 " pdb=" C HIS D 279 " pdb=" CB HIS D 279 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA HIS B 279 " pdb=" N HIS B 279 " pdb=" C HIS B 279 " pdb=" CB HIS B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+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 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2481 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO D 320 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 319 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 320 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 319 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 320 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " 0.059 5.00e-02 4.00e+02 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5815 2.90 - 3.40: 17126 3.40 - 3.90: 25485 3.90 - 4.40: 29039 4.40 - 4.90: 45820 Nonbonded interactions: 123285 Sorted by model distance: nonbonded pdb=" O LYS C 261 " pdb=" OG SER C 264 " model vdw 2.399 2.440 nonbonded pdb=" O LYS D 261 " pdb=" OG SER D 264 " model vdw 2.399 2.440 nonbonded pdb=" O LYS A 261 " pdb=" OG SER A 264 " model vdw 2.399 2.440 nonbonded pdb=" O LYS B 261 " pdb=" OG SER B 264 " model vdw 2.400 2.440 nonbonded pdb=" O ASP C 225 " pdb=" OG SER C 228 " model vdw 2.447 2.440 ... (remaining 123280 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' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 C 10156 2.51 5 N 2688 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.770 Check model and map are aligned: 0.230 Process input model: 41.140 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 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 : 0.007 0.044 16016 Z= 0.485 Angle : 1.403 6.987 21800 Z= 1.083 Chirality : 0.073 0.285 2484 Planarity : 0.006 0.112 2748 Dihedral : 12.411 158.034 5388 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 1992 helix: 1.89 (0.12), residues: 1380 sheet: 0.47 (0.47), residues: 100 loop : -1.97 (0.24), residues: 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.2662 time to fit residues: 202.7989 Evaluate side-chains 327 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 D 398 GLN D 421 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5322 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16016 Z= 0.193 Angle : 0.565 8.272 21800 Z= 0.293 Chirality : 0.040 0.158 2484 Planarity : 0.005 0.068 2748 Dihedral : 11.672 164.016 2304 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 2.63 % 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: 3.19 (0.19), residues: 1992 helix: 3.45 (0.13), residues: 1376 sheet: 0.26 (0.45), residues: 96 loop : -1.50 (0.25), residues: 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 384 time to evaluate : 1.845 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 398 average time/residue: 0.2282 time to fit residues: 143.0802 Evaluate side-chains 348 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 330 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1374 time to fit residues: 7.2702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 51 optimal weight: 30.0000 chunk 185 optimal weight: 0.7980 chunk 200 optimal weight: 0.3980 chunk 165 optimal weight: 0.7980 chunk 184 optimal weight: 0.0170 chunk 63 optimal weight: 0.9990 chunk 148 optimal weight: 0.0570 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 286 HIS A 408 GLN A 517 HIS B 517 HIS C 179 ASN C 408 GLN C 421 HIS D 408 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5314 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16016 Z= 0.160 Angle : 0.529 13.199 21800 Z= 0.266 Chirality : 0.038 0.147 2484 Planarity : 0.004 0.053 2748 Dihedral : 11.176 161.351 2304 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.21 % 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: 2.99 (0.19), residues: 1992 helix: 3.15 (0.13), residues: 1400 sheet: 0.54 (0.48), residues: 96 loop : -1.41 (0.27), residues: 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 360 time to evaluate : 1.995 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 369 average time/residue: 0.2206 time to fit residues: 129.3038 Evaluate side-chains 335 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 327 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1391 time to fit residues: 4.4501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 0.0270 chunk 53 optimal weight: 3.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 408 GLN D 517 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 16016 Z= 0.189 Angle : 0.519 10.763 21800 Z= 0.260 Chirality : 0.038 0.142 2484 Planarity : 0.003 0.045 2748 Dihedral : 10.879 152.092 2304 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 1.78 % 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: 2.81 (0.19), residues: 1992 helix: 2.90 (0.13), residues: 1408 sheet: 0.74 (0.51), residues: 96 loop : -1.19 (0.27), residues: 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 340 time to evaluate : 1.842 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 352 average time/residue: 0.2297 time to fit residues: 128.2311 Evaluate side-chains 342 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 327 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1463 time to fit residues: 6.6591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 136 optimal weight: 0.0870 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 overall best weight: 3.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 300 ASN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 16016 Z= 0.392 Angle : 0.600 11.845 21800 Z= 0.309 Chirality : 0.041 0.166 2484 Planarity : 0.004 0.044 2748 Dihedral : 10.825 149.902 2304 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.99 % 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: 2.46 (0.19), residues: 1992 helix: 2.62 (0.13), residues: 1396 sheet: 0.86 (0.52), residues: 96 loop : -1.22 (0.27), residues: 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 323 time to evaluate : 1.955 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 332 average time/residue: 0.2248 time to fit residues: 117.9100 Evaluate side-chains 336 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 319 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1428 time to fit residues: 6.9833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5304 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16016 Z= 0.187 Angle : 0.516 8.361 21800 Z= 0.261 Chirality : 0.038 0.155 2484 Planarity : 0.003 0.040 2748 Dihedral : 10.832 151.341 2304 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.56 % 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: 2.52 (0.19), residues: 1992 helix: 2.62 (0.13), residues: 1396 sheet: 0.79 (0.53), residues: 96 loop : -1.06 (0.27), residues: 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 331 time to evaluate : 1.729 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 339 average time/residue: 0.2307 time to fit residues: 123.5856 Evaluate side-chains 341 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 327 time to evaluate : 1.840 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1528 time to fit residues: 6.5066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 110 optimal weight: 0.0070 chunk 196 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5311 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 16016 Z= 0.247 Angle : 0.534 8.546 21800 Z= 0.271 Chirality : 0.038 0.146 2484 Planarity : 0.003 0.036 2748 Dihedral : 10.778 150.379 2304 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.56 % 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: 2.50 (0.19), residues: 1992 helix: 2.60 (0.14), residues: 1396 sheet: 0.80 (0.53), residues: 96 loop : -1.04 (0.27), residues: 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 326 time to evaluate : 1.821 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 329 average time/residue: 0.2256 time to fit residues: 118.2405 Evaluate side-chains 323 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 311 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1440 time to fit residues: 5.8675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.0370 chunk 133 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS D 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5304 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16016 Z= 0.181 Angle : 0.517 8.861 21800 Z= 0.260 Chirality : 0.037 0.158 2484 Planarity : 0.003 0.051 2748 Dihedral : 10.773 150.485 2304 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.64 % 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: 2.48 (0.19), residues: 1992 helix: 2.53 (0.13), residues: 1404 sheet: 0.82 (0.53), residues: 96 loop : -0.93 (0.28), residues: 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 333 time to evaluate : 1.758 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 335 average time/residue: 0.2348 time to fit residues: 123.5982 Evaluate side-chains 321 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 314 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1465 time to fit residues: 4.3816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 286 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS D 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16016 Z= 0.193 Angle : 0.524 9.352 21800 Z= 0.263 Chirality : 0.037 0.165 2484 Planarity : 0.003 0.035 2748 Dihedral : 10.748 149.825 2304 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.64 % 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: 2.50 (0.19), residues: 1992 helix: 2.57 (0.13), residues: 1396 sheet: 0.92 (0.54), residues: 96 loop : -0.98 (0.27), residues: 500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 325 time to evaluate : 2.029 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 328 average time/residue: 0.2282 time to fit residues: 118.9650 Evaluate side-chains 317 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 312 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1383 time to fit residues: 3.6779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS B 156 ASN B 286 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS D 156 ASN D 286 HIS ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5312 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 16016 Z= 0.300 Angle : 0.570 9.665 21800 Z= 0.290 Chirality : 0.039 0.194 2484 Planarity : 0.004 0.036 2748 Dihedral : 10.745 149.283 2304 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.50 % 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: 2.46 (0.19), residues: 1992 helix: 2.50 (0.14), residues: 1396 sheet: 1.59 (0.53), residues: 88 loop : -0.94 (0.27), residues: 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 330 time to evaluate : 1.710 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 331 average time/residue: 0.2242 time to fit residues: 118.5373 Evaluate side-chains 329 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 326 time to evaluate : 1.874 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1383 time to fit residues: 3.4398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 50.0000 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 166 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 142 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS B 156 ASN B 286 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS D 156 ASN D 286 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.093728 restraints weight = 31030.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096543 restraints weight = 15088.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098233 restraints weight = 9727.402| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 16016 Z= 0.165 Angle : 0.532 9.756 21800 Z= 0.267 Chirality : 0.038 0.174 2484 Planarity : 0.003 0.034 2748 Dihedral : 10.775 150.264 2304 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.36 % 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: 2.44 (0.19), residues: 1992 helix: 2.51 (0.14), residues: 1392 sheet: 0.94 (0.53), residues: 96 loop : -0.89 (0.27), residues: 504 =============================================================================== Job complete usr+sys time: 3046.94 seconds wall clock time: 55 minutes 46.58 seconds (3346.58 seconds total)