Starting phenix.real_space_refine on Fri Feb 16 14:56:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2024/5u6p_8512_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2024/5u6p_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_2024/5u6p_8512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2024/5u6p_8512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2024/5u6p_8512_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/02_2024/5u6p_8512_updated.pdb" } resolution = 3.51 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= 0.007 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 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. 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-5238/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: 8.25, per 1000 atoms: 0.53 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: 6.64 Conformation dependent library (CDL) restraints added in 3.1 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: 3.61 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: 4.71 Time building geometry restraints manager: 7.05 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 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: 0.800 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: 0.020 Extract box with map and model: 3.970 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 44.250 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 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 % Allowed : 1.21 % Favored : 98.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 281 HIS 0.008 0.002 HIS D 437 PHE 0.027 0.002 PHE A 569 TYR 0.027 0.002 TYR C 411 ARG 0.005 0.001 ARG B 112 *********************** 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 : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8142 (mt) cc_final: 0.7785 (tt) REVERT: A 234 TYR cc_start: 0.6663 (m-80) cc_final: 0.5665 (t80) REVERT: A 236 PHE cc_start: 0.8369 (t80) cc_final: 0.8137 (t80) REVERT: A 439 TYR cc_start: 0.6267 (m-80) cc_final: 0.6007 (m-80) REVERT: B 135 ILE cc_start: 0.8309 (mt) cc_final: 0.8069 (tt) REVERT: B 152 MET cc_start: 0.6683 (mmm) cc_final: 0.6314 (tpt) REVERT: B 234 TYR cc_start: 0.6469 (m-80) cc_final: 0.5524 (t80) REVERT: B 445 ASP cc_start: 0.6626 (t0) cc_final: 0.6413 (p0) REVERT: B 482 ASN cc_start: 0.8055 (m110) cc_final: 0.7673 (t0) REVERT: B 485 THR cc_start: 0.8331 (m) cc_final: 0.8108 (p) REVERT: C 135 ILE cc_start: 0.8233 (mt) cc_final: 0.7939 (tt) REVERT: C 152 MET cc_start: 0.6730 (mmm) cc_final: 0.6341 (tpt) REVERT: C 217 TYR cc_start: 0.6281 (t80) cc_final: 0.6046 (t80) REVERT: C 234 TYR cc_start: 0.6468 (m-80) cc_final: 0.5654 (t80) REVERT: C 287 MET cc_start: 0.6196 (mmm) cc_final: 0.5872 (mmt) REVERT: C 336 MET cc_start: 0.7088 (ptm) cc_final: 0.6883 (ptp) REVERT: C 445 ASP cc_start: 0.6820 (t0) cc_final: 0.6513 (p0) REVERT: D 135 ILE cc_start: 0.8345 (mt) cc_final: 0.8092 (tt) REVERT: D 152 MET cc_start: 0.6796 (mmm) cc_final: 0.6433 (tpt) REVERT: D 217 TYR cc_start: 0.5843 (t80) cc_final: 0.5615 (t80) REVERT: D 233 ASP cc_start: 0.6993 (p0) cc_final: 0.6099 (p0) REVERT: D 234 TYR cc_start: 0.6374 (m-80) cc_final: 0.5615 (t80) REVERT: D 336 MET cc_start: 0.7020 (ptm) cc_final: 0.6819 (ptp) REVERT: D 445 ASP cc_start: 0.6655 (t0) cc_final: 0.6452 (p0) REVERT: D 482 ASN cc_start: 0.7800 (m110) cc_final: 0.7434 (m-40) REVERT: D 485 THR cc_start: 0.8419 (m) cc_final: 0.8207 (p) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.2644 time to fit residues: 201.2175 Evaluate side-chains 338 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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: 0.0870 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 0.0870 chunk 61 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.5395 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16016 Z= 0.179 Angle : 0.558 8.268 21800 Z= 0.290 Chirality : 0.040 0.150 2484 Planarity : 0.005 0.067 2748 Dihedral : 11.664 164.098 2304 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.34 % Allowed : 10.09 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.19), residues: 1992 helix: 3.48 (0.13), residues: 1384 sheet: 0.30 (0.45), residues: 96 loop : -1.47 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 281 HIS 0.007 0.001 HIS B 432 PHE 0.031 0.002 PHE D 186 TYR 0.018 0.001 TYR D 411 ARG 0.013 0.001 ARG B 112 *********************** 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 429 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 396 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: A 192 MET cc_start: 0.6908 (tpp) cc_final: 0.6653 (ttm) REVERT: A 233 ASP cc_start: 0.6656 (p0) cc_final: 0.5891 (p0) REVERT: A 234 TYR cc_start: 0.6691 (m-80) cc_final: 0.5726 (t80) REVERT: A 236 PHE cc_start: 0.8319 (t80) cc_final: 0.8065 (t80) REVERT: A 436 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 439 TYR cc_start: 0.6276 (m-80) cc_final: 0.5935 (m-80) REVERT: B 140 ASP cc_start: 0.7490 (m-30) cc_final: 0.7210 (t0) REVERT: B 234 TYR cc_start: 0.6378 (m-80) cc_final: 0.5351 (t80) REVERT: B 445 ASP cc_start: 0.6387 (t0) cc_final: 0.6133 (p0) REVERT: B 482 ASN cc_start: 0.8025 (m110) cc_final: 0.7587 (t0) REVERT: C 234 TYR cc_start: 0.6512 (m-80) cc_final: 0.5633 (t80) REVERT: C 445 ASP cc_start: 0.6422 (t0) cc_final: 0.6149 (p0) REVERT: C 482 ASN cc_start: 0.7686 (m110) cc_final: 0.7441 (m-40) REVERT: D 234 TYR cc_start: 0.6397 (m-80) cc_final: 0.5393 (t80) REVERT: D 287 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.5380 (tpt) REVERT: D 445 ASP cc_start: 0.6481 (t0) cc_final: 0.5874 (p0) REVERT: D 482 ASN cc_start: 0.7906 (m110) cc_final: 0.7469 (m-40) outliers start: 33 outliers final: 14 residues processed: 408 average time/residue: 0.2396 time to fit residues: 156.4488 Evaluate side-chains 360 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 345 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 378 SER 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: 0.7980 chunk 154 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 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: 0.5394 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16016 Z= 0.184 Angle : 0.530 13.118 21800 Z= 0.267 Chirality : 0.039 0.147 2484 Planarity : 0.004 0.053 2748 Dihedral : 11.158 160.759 2304 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.20 % Allowed : 12.22 % Favored : 85.58 % 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: 3.05 (0.19), residues: 1992 helix: 3.23 (0.13), residues: 1392 sheet: 0.51 (0.48), residues: 96 loop : -1.42 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 281 HIS 0.006 0.001 HIS A 517 PHE 0.018 0.001 PHE B 569 TYR 0.018 0.001 TYR B 217 ARG 0.007 0.000 ARG B 112 *********************** 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 403 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 372 time to evaluate : 1.865 Fit side-chains REVERT: A 234 TYR cc_start: 0.6694 (m-80) cc_final: 0.5682 (t80) REVERT: A 236 PHE cc_start: 0.8255 (t80) cc_final: 0.8005 (t80) REVERT: A 289 TYR cc_start: 0.5524 (m-80) cc_final: 0.5080 (m-10) REVERT: A 439 TYR cc_start: 0.6031 (m-80) cc_final: 0.5546 (m-80) REVERT: B 234 TYR cc_start: 0.6288 (m-80) cc_final: 0.5285 (t80) REVERT: B 482 ASN cc_start: 0.7877 (m110) cc_final: 0.7634 (m-40) REVERT: C 234 TYR cc_start: 0.6509 (m-80) cc_final: 0.5638 (t80) REVERT: C 445 ASP cc_start: 0.6643 (t0) cc_final: 0.6364 (p0) REVERT: C 517 HIS cc_start: 0.6640 (m-70) cc_final: 0.6379 (m90) REVERT: D 234 TYR cc_start: 0.6514 (m-80) cc_final: 0.5466 (t80) REVERT: D 445 ASP cc_start: 0.6484 (t0) cc_final: 0.6237 (p0) REVERT: D 482 ASN cc_start: 0.7784 (m110) cc_final: 0.7544 (m-40) outliers start: 31 outliers final: 19 residues processed: 388 average time/residue: 0.2240 time to fit residues: 136.9575 Evaluate side-chains 350 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 331 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 0.0170 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 408 GLN C 300 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16016 Z= 0.244 Angle : 0.537 10.522 21800 Z= 0.273 Chirality : 0.039 0.152 2484 Planarity : 0.004 0.045 2748 Dihedral : 10.847 151.423 2304 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.84 % Allowed : 14.63 % Favored : 82.53 % 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: 2.74 (0.19), residues: 1992 helix: 2.88 (0.13), residues: 1400 sheet: 0.78 (0.52), residues: 96 loop : -1.30 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP B 281 HIS 0.013 0.001 HIS D 432 PHE 0.015 0.001 PHE C 569 TYR 0.018 0.001 TYR D 411 ARG 0.007 0.001 ARG A 112 *********************** 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 377 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 337 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.7371 (mmm) cc_final: 0.7145 (tpp) REVERT: A 217 TYR cc_start: 0.5570 (t80) cc_final: 0.5244 (t80) REVERT: A 234 TYR cc_start: 0.6813 (m-80) cc_final: 0.5801 (t80) REVERT: A 236 PHE cc_start: 0.8267 (t80) cc_final: 0.8011 (t80) REVERT: A 289 TYR cc_start: 0.5803 (m-80) cc_final: 0.5436 (m-10) REVERT: B 234 TYR cc_start: 0.6525 (m-80) cc_final: 0.5523 (t80) REVERT: B 482 ASN cc_start: 0.7876 (m110) cc_final: 0.7633 (m-40) REVERT: C 217 TYR cc_start: 0.5750 (t80) cc_final: 0.5501 (t80) REVERT: C 234 TYR cc_start: 0.6542 (m-80) cc_final: 0.5703 (t80) REVERT: C 517 HIS cc_start: 0.6623 (m-70) cc_final: 0.6375 (m90) REVERT: D 217 TYR cc_start: 0.5784 (t80) cc_final: 0.5562 (t80) REVERT: D 234 TYR cc_start: 0.6526 (m-80) cc_final: 0.5667 (t80) REVERT: D 482 ASN cc_start: 0.7754 (m110) cc_final: 0.7516 (m-40) outliers start: 40 outliers final: 30 residues processed: 354 average time/residue: 0.2233 time to fit residues: 124.2752 Evaluate side-chains 354 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 324 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 8.9990 chunk 111 optimal weight: 0.0980 chunk 2 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5408 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 16016 Z= 0.501 Angle : 0.668 7.680 21800 Z= 0.348 Chirality : 0.044 0.195 2484 Planarity : 0.004 0.041 2748 Dihedral : 10.890 149.298 2304 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.98 % Allowed : 14.70 % Favored : 81.32 % 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: 1.95 (0.18), residues: 1992 helix: 2.22 (0.13), residues: 1396 sheet: 0.57 (0.52), residues: 88 loop : -1.31 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.004 TRP D 281 HIS 0.010 0.002 HIS D 355 PHE 0.016 0.002 PHE D 569 TYR 0.019 0.002 TYR B 411 ARG 0.006 0.001 ARG B 112 *********************** 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 374 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 318 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 TYR cc_start: 0.6840 (m-80) cc_final: 0.5837 (t80) REVERT: A 236 PHE cc_start: 0.8399 (t80) cc_final: 0.8175 (t80) REVERT: A 289 TYR cc_start: 0.5699 (m-80) cc_final: 0.5406 (m-10) REVERT: A 439 TYR cc_start: 0.5990 (m-80) cc_final: 0.5596 (m-80) REVERT: B 234 TYR cc_start: 0.6622 (m-80) cc_final: 0.5714 (t80) REVERT: B 289 TYR cc_start: 0.5649 (m-80) cc_final: 0.5440 (m-80) REVERT: B 482 ASN cc_start: 0.7739 (m110) cc_final: 0.7500 (m-40) REVERT: C 234 TYR cc_start: 0.6674 (m-80) cc_final: 0.5757 (t80) REVERT: C 517 HIS cc_start: 0.6344 (m-70) cc_final: 0.6110 (m90) REVERT: D 234 TYR cc_start: 0.6671 (m-80) cc_final: 0.5698 (t80) REVERT: D 289 TYR cc_start: 0.5539 (m-80) cc_final: 0.5330 (m-80) REVERT: D 482 ASN cc_start: 0.7662 (m110) cc_final: 0.7438 (m-40) outliers start: 56 outliers final: 36 residues processed: 342 average time/residue: 0.2239 time to fit residues: 120.7487 Evaluate side-chains 345 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 309 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 385 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 8.9990 chunk 177 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 163 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5378 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16016 Z= 0.164 Angle : 0.517 8.430 21800 Z= 0.261 Chirality : 0.038 0.153 2484 Planarity : 0.003 0.038 2748 Dihedral : 10.906 152.164 2304 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.49 % Allowed : 16.26 % Favored : 81.25 % 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: 1992 helix: 2.46 (0.13), residues: 1404 sheet: 0.70 (0.52), residues: 96 loop : -1.22 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 281 HIS 0.005 0.001 HIS D 432 PHE 0.014 0.001 PHE C 317 TYR 0.022 0.001 TYR C 217 ARG 0.005 0.000 ARG A 560 *********************** 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 377 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 342 time to evaluate : 2.015 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7095 (t0) cc_final: 0.6858 (t0) REVERT: A 217 TYR cc_start: 0.5957 (t80) cc_final: 0.5659 (t80) REVERT: A 234 TYR cc_start: 0.6829 (m-80) cc_final: 0.5750 (t80) REVERT: A 236 PHE cc_start: 0.8276 (t80) cc_final: 0.8028 (t80) REVERT: A 289 TYR cc_start: 0.5804 (m-80) cc_final: 0.5529 (m-10) REVERT: A 439 TYR cc_start: 0.6117 (m-80) cc_final: 0.5591 (m-80) REVERT: B 217 TYR cc_start: 0.5706 (t80) cc_final: 0.5187 (t80) REVERT: B 234 TYR cc_start: 0.6631 (m-80) cc_final: 0.5716 (t80) REVERT: B 289 TYR cc_start: 0.5923 (m-80) cc_final: 0.5538 (m-80) REVERT: B 482 ASN cc_start: 0.7790 (m110) cc_final: 0.7534 (m-40) REVERT: C 140 ASP cc_start: 0.6924 (t0) cc_final: 0.6699 (t0) REVERT: C 217 TYR cc_start: 0.5340 (t80) cc_final: 0.5017 (t80) REVERT: C 234 TYR cc_start: 0.6673 (m-80) cc_final: 0.5760 (t80) REVERT: C 287 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5844 (tpp) REVERT: C 289 TYR cc_start: 0.5952 (m-80) cc_final: 0.5527 (m-10) REVERT: C 517 HIS cc_start: 0.6543 (m-70) cc_final: 0.6272 (m90) REVERT: D 234 TYR cc_start: 0.6642 (m-80) cc_final: 0.5743 (t80) REVERT: D 482 ASN cc_start: 0.7646 (m110) cc_final: 0.7399 (m-40) outliers start: 35 outliers final: 24 residues processed: 358 average time/residue: 0.2221 time to fit residues: 126.2567 Evaluate side-chains 344 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 319 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 0.0770 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5378 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16016 Z= 0.157 Angle : 0.502 8.434 21800 Z= 0.253 Chirality : 0.037 0.167 2484 Planarity : 0.003 0.035 2748 Dihedral : 10.780 150.687 2304 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.92 % Allowed : 17.19 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.19), residues: 1992 helix: 2.56 (0.13), residues: 1400 sheet: 0.73 (0.52), residues: 96 loop : -1.06 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 281 HIS 0.005 0.001 HIS D 432 PHE 0.028 0.001 PHE B 143 TYR 0.015 0.001 TYR C 217 ARG 0.005 0.000 ARG A 560 *********************** 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 356 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 329 time to evaluate : 1.819 Fit side-chains revert: symmetry clash REVERT: A 217 TYR cc_start: 0.6126 (t80) cc_final: 0.5881 (t80) REVERT: A 234 TYR cc_start: 0.6824 (m-80) cc_final: 0.5774 (t80) REVERT: A 236 PHE cc_start: 0.8267 (t80) cc_final: 0.8015 (t80) REVERT: A 289 TYR cc_start: 0.5782 (m-80) cc_final: 0.5501 (m-10) REVERT: A 439 TYR cc_start: 0.5980 (m-80) cc_final: 0.5528 (m-80) REVERT: B 217 TYR cc_start: 0.5663 (t80) cc_final: 0.5114 (t80) REVERT: B 234 TYR cc_start: 0.6659 (m-80) cc_final: 0.5753 (t80) REVERT: B 482 ASN cc_start: 0.7792 (m110) cc_final: 0.7541 (m-40) REVERT: C 217 TYR cc_start: 0.5695 (t80) cc_final: 0.5358 (t80) REVERT: C 234 TYR cc_start: 0.6661 (m-80) cc_final: 0.5693 (t80) REVERT: C 287 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.6026 (tpp) REVERT: C 289 TYR cc_start: 0.5976 (m-80) cc_final: 0.5520 (m-10) REVERT: C 517 HIS cc_start: 0.6534 (m-70) cc_final: 0.6312 (m90) REVERT: D 217 TYR cc_start: 0.5496 (t80) cc_final: 0.5092 (t80) REVERT: D 234 TYR cc_start: 0.6685 (m-80) cc_final: 0.5713 (t80) REVERT: D 482 ASN cc_start: 0.7581 (m110) cc_final: 0.7329 (m-40) outliers start: 27 outliers final: 17 residues processed: 343 average time/residue: 0.2230 time to fit residues: 121.3939 Evaluate side-chains 337 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 319 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 380 ILE 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: 1.9990 chunk 117 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 154 optimal weight: 0.5980 chunk 178 optimal weight: 7.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16016 Z= 0.176 Angle : 0.506 8.843 21800 Z= 0.255 Chirality : 0.037 0.168 2484 Planarity : 0.003 0.034 2748 Dihedral : 10.731 149.732 2304 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.13 % Allowed : 17.26 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.19), residues: 1992 helix: 2.55 (0.13), residues: 1400 sheet: 0.82 (0.53), residues: 96 loop : -1.03 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 281 HIS 0.005 0.001 HIS C 432 PHE 0.016 0.001 PHE B 143 TYR 0.013 0.001 TYR B 411 ARG 0.005 0.000 ARG D 560 *********************** 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 354 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 324 time to evaluate : 1.843 Fit side-chains revert: symmetry clash REVERT: A 217 TYR cc_start: 0.6150 (t80) cc_final: 0.5839 (t80) REVERT: A 234 TYR cc_start: 0.6826 (m-80) cc_final: 0.5779 (t80) REVERT: A 236 PHE cc_start: 0.8263 (t80) cc_final: 0.8013 (t80) REVERT: B 217 TYR cc_start: 0.5662 (t80) cc_final: 0.5069 (t80) REVERT: B 234 TYR cc_start: 0.6649 (m-80) cc_final: 0.5762 (t80) REVERT: B 289 TYR cc_start: 0.5917 (m-80) cc_final: 0.5455 (m-10) REVERT: B 482 ASN cc_start: 0.7793 (m110) cc_final: 0.7546 (m-40) REVERT: C 234 TYR cc_start: 0.6712 (m-80) cc_final: 0.5697 (t80) REVERT: C 287 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.6041 (tpp) REVERT: C 289 TYR cc_start: 0.6001 (m-80) cc_final: 0.5526 (m-10) REVERT: C 517 HIS cc_start: 0.6279 (m-70) cc_final: 0.6073 (m90) REVERT: D 234 TYR cc_start: 0.6682 (m-80) cc_final: 0.5723 (t80) REVERT: D 482 ASN cc_start: 0.7585 (m110) cc_final: 0.7331 (m-40) outliers start: 30 outliers final: 22 residues processed: 336 average time/residue: 0.2228 time to fit residues: 119.0907 Evaluate side-chains 337 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 314 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 397 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 HIS B 463 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16016 Z= 0.174 Angle : 0.515 9.663 21800 Z= 0.258 Chirality : 0.038 0.180 2484 Planarity : 0.003 0.034 2748 Dihedral : 10.720 149.589 2304 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.13 % Allowed : 17.26 % Favored : 80.61 % 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: 1992 helix: 2.48 (0.13), residues: 1404 sheet: 0.82 (0.53), residues: 96 loop : -1.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 281 HIS 0.006 0.001 HIS C 432 PHE 0.013 0.001 PHE A 317 TYR 0.014 0.001 TYR A 289 ARG 0.005 0.000 ARG A 112 *********************** 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 361 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 331 time to evaluate : 1.969 Fit side-chains revert: symmetry clash REVERT: A 217 TYR cc_start: 0.6119 (t80) cc_final: 0.5805 (t80) REVERT: A 234 TYR cc_start: 0.6820 (m-80) cc_final: 0.5775 (t80) REVERT: A 236 PHE cc_start: 0.8116 (t80) cc_final: 0.7858 (t80) REVERT: B 217 TYR cc_start: 0.5620 (t80) cc_final: 0.5035 (t80) REVERT: B 234 TYR cc_start: 0.6639 (m-80) cc_final: 0.5719 (t80) REVERT: B 289 TYR cc_start: 0.5886 (m-80) cc_final: 0.5425 (m-10) REVERT: B 482 ASN cc_start: 0.7794 (m110) cc_final: 0.7549 (m-40) REVERT: C 217 TYR cc_start: 0.5779 (t80) cc_final: 0.5373 (t80) REVERT: C 234 TYR cc_start: 0.6709 (m-80) cc_final: 0.5698 (t80) REVERT: C 287 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.6055 (tpt) REVERT: C 289 TYR cc_start: 0.6000 (m-80) cc_final: 0.5534 (m-10) REVERT: C 517 HIS cc_start: 0.6365 (m-70) cc_final: 0.6163 (m90) REVERT: D 234 TYR cc_start: 0.6677 (m-80) cc_final: 0.5715 (t80) REVERT: D 281 TRP cc_start: 0.5863 (m100) cc_final: 0.5621 (m100) REVERT: D 289 TYR cc_start: 0.5733 (m-80) cc_final: 0.5269 (m-10) REVERT: D 482 ASN cc_start: 0.7589 (m110) cc_final: 0.7332 (m-40) outliers start: 30 outliers final: 21 residues processed: 345 average time/residue: 0.2432 time to fit residues: 134.1411 Evaluate side-chains 351 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 329 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS B 286 HIS ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16016 Z= 0.311 Angle : 0.568 9.521 21800 Z= 0.289 Chirality : 0.039 0.190 2484 Planarity : 0.003 0.032 2748 Dihedral : 10.715 148.812 2304 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.92 % Allowed : 17.61 % Favored : 80.47 % 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: 2.27 (0.19), residues: 1992 helix: 2.36 (0.14), residues: 1404 sheet: 1.51 (0.52), residues: 88 loop : -1.07 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP B 281 HIS 0.006 0.001 HIS C 432 PHE 0.014 0.001 PHE D 317 TYR 0.012 0.001 TYR A 411 ARG 0.005 0.001 ARG A 267 ********************** 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 354 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 327 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 217 TYR cc_start: 0.6102 (t80) cc_final: 0.5822 (t80) REVERT: A 234 TYR cc_start: 0.6937 (m-80) cc_final: 0.5915 (t80) REVERT: A 236 PHE cc_start: 0.8215 (t80) cc_final: 0.7975 (t80) REVERT: A 482 ASN cc_start: 0.7428 (m110) cc_final: 0.7225 (m-40) REVERT: B 217 TYR cc_start: 0.5999 (t80) cc_final: 0.5480 (t80) REVERT: B 234 TYR cc_start: 0.6682 (m-80) cc_final: 0.5710 (t80) REVERT: B 289 TYR cc_start: 0.5754 (m-80) cc_final: 0.5334 (m-10) REVERT: B 482 ASN cc_start: 0.7665 (m110) cc_final: 0.7408 (m-40) REVERT: C 234 TYR cc_start: 0.6718 (m-80) cc_final: 0.5709 (t80) REVERT: C 287 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.6096 (tpt) REVERT: C 517 HIS cc_start: 0.6258 (m-70) cc_final: 0.6022 (m90) REVERT: D 234 TYR cc_start: 0.6686 (m-80) cc_final: 0.5741 (t80) REVERT: D 482 ASN cc_start: 0.7502 (m110) cc_final: 0.7260 (m-40) outliers start: 27 outliers final: 24 residues processed: 339 average time/residue: 0.2325 time to fit residues: 126.6411 Evaluate side-chains 346 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 321 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 397 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.6980 chunk 49 optimal weight: 50.0000 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS B 286 HIS D 286 HIS ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.091552 restraints weight = 31212.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094198 restraints weight = 15603.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095869 restraints weight = 10258.823| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16016 Z= 0.254 Angle : 0.557 9.791 21800 Z= 0.282 Chirality : 0.039 0.193 2484 Planarity : 0.003 0.033 2748 Dihedral : 10.758 149.339 2304 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.85 % Allowed : 18.18 % Favored : 79.97 % 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: 2.15 (0.19), residues: 1992 helix: 2.26 (0.14), residues: 1408 sheet: 1.82 (0.52), residues: 92 loop : -1.23 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP D 281 HIS 0.006 0.001 HIS C 432 PHE 0.013 0.001 PHE C 317 TYR 0.013 0.001 TYR B 411 ARG 0.005 0.000 ARG A 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3240.78 seconds wall clock time: 59 minutes 47.47 seconds (3587.47 seconds total)