Starting phenix.real_space_refine (version: dev) on Fri Feb 24 23:11:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/02_2023/5yys_6859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/02_2023/5yys_6859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/02_2023/5yys_6859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/02_2023/5yys_6859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/02_2023/5yys_6859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/02_2023/5yys_6859.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 80": "NH1" <-> "NH2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 787": "NH1" <-> "NH2" Residue "B TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 571": "NH1" <-> "NH2" Residue "C ARG 588": "NH1" <-> "NH2" Residue "C TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 787": "NH1" <-> "NH2" Residue "C TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 571": "NH1" <-> "NH2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 787": "NH1" <-> "NH2" Residue "D TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24044 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6011 Classifications: {'peptide': 811} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'CIS': 36, 'PCIS': 2, 'PTRANS': 44, 'TRANS': 728} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 204 Chain: "B" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6011 Classifications: {'peptide': 811} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'CIS': 36, 'PCIS': 2, 'PTRANS': 44, 'TRANS': 728} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 204 Chain: "C" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6011 Classifications: {'peptide': 811} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'CIS': 36, 'PCIS': 2, 'PTRANS': 44, 'TRANS': 728} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 204 Chain: "D" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6011 Classifications: {'peptide': 811} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'CIS': 36, 'PCIS': 2, 'PTRANS': 44, 'TRANS': 728} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 204 Time building chain proxies: 13.64, per 1000 atoms: 0.57 Number of scatterers: 24044 At special positions: 0 Unit cell: (115.7, 130, 209.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 4496 8.00 N 4148 7.00 C 15312 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: 10.69 Conformation dependent library (CDL) restraints added in 3.8 seconds 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 20 sheets defined 34.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 107 through 119 Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 275 through 284 removed outlier: 4.018A pdb=" N LEU A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 removed outlier: 4.052A pdb=" N GLY A 385 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A 386 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU A 387 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 388 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 389 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.929A pdb=" N ARG A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 527 through 545 Processing helix chain 'A' and resid 548 through 566 removed outlier: 3.583A pdb=" N ASP A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 675 removed outlier: 3.540A pdb=" N ALA A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 717 through 734 Processing helix chain 'A' and resid 739 through 755 removed outlier: 3.914A pdb=" N LEU A 753 " --> pdb=" O VAL A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.573A pdb=" N TYR A 764 " --> pdb=" O TRP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 830 through 852 removed outlier: 3.686A pdb=" N ASN A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 871 Processing helix chain 'A' and resid 878 through 887 removed outlier: 3.760A pdb=" N GLU A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 925 Processing helix chain 'B' and resid 107 through 119 Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 275 through 284 removed outlier: 4.019A pdb=" N LEU B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 389 removed outlier: 4.053A pdb=" N GLY B 385 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 386 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU B 387 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG B 388 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 389 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.928A pdb=" N ARG B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 502 through 509 Processing helix chain 'B' and resid 516 through 522 Processing helix chain 'B' and resid 527 through 545 Processing helix chain 'B' and resid 548 through 566 removed outlier: 3.583A pdb=" N ASP B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 675 removed outlier: 3.540A pdb=" N ALA B 672 " --> pdb=" O SER B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 717 through 734 Processing helix chain 'B' and resid 739 through 755 removed outlier: 3.914A pdb=" N LEU B 753 " --> pdb=" O VAL B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 766 removed outlier: 3.572A pdb=" N TYR B 764 " --> pdb=" O TRP B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 830 through 852 removed outlier: 3.687A pdb=" N ASN B 834 " --> pdb=" O SER B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 871 Processing helix chain 'B' and resid 878 through 887 removed outlier: 3.760A pdb=" N GLU B 882 " --> pdb=" O PRO B 878 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 925 Processing helix chain 'C' and resid 107 through 119 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 275 through 284 removed outlier: 4.018A pdb=" N LEU C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 389 removed outlier: 4.052A pdb=" N GLY C 385 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C 386 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU C 387 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG C 388 " --> pdb=" O GLY C 385 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 389 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.928A pdb=" N ARG C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 516 through 522 Processing helix chain 'C' and resid 527 through 545 Processing helix chain 'C' and resid 548 through 566 removed outlier: 3.583A pdb=" N ASP C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 675 removed outlier: 3.539A pdb=" N ALA C 672 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 717 through 734 Processing helix chain 'C' and resid 739 through 755 removed outlier: 3.915A pdb=" N LEU C 753 " --> pdb=" O VAL C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 766 removed outlier: 3.572A pdb=" N TYR C 764 " --> pdb=" O TRP C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 Processing helix chain 'C' and resid 830 through 852 removed outlier: 3.686A pdb=" N ASN C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 871 Processing helix chain 'C' and resid 878 through 887 removed outlier: 3.760A pdb=" N GLU C 882 " --> pdb=" O PRO C 878 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 887 " --> pdb=" O ALA C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 925 Processing helix chain 'D' and resid 107 through 119 Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 189 through 195 Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 275 through 284 removed outlier: 4.019A pdb=" N LEU D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 389 removed outlier: 4.053A pdb=" N GLY D 385 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D 386 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU D 387 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG D 388 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 389 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 479 removed outlier: 3.929A pdb=" N ARG D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 516 through 522 Processing helix chain 'D' and resid 527 through 545 Processing helix chain 'D' and resid 548 through 566 removed outlier: 3.583A pdb=" N ASP D 566 " --> pdb=" O ASP D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.539A pdb=" N ALA D 672 " --> pdb=" O SER D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 717 through 734 Processing helix chain 'D' and resid 739 through 755 removed outlier: 3.914A pdb=" N LEU D 753 " --> pdb=" O VAL D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 766 removed outlier: 3.573A pdb=" N TYR D 764 " --> pdb=" O TRP D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 824 Processing helix chain 'D' and resid 830 through 852 removed outlier: 3.687A pdb=" N ASN D 834 " --> pdb=" O SER D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 871 Processing helix chain 'D' and resid 878 through 887 removed outlier: 3.760A pdb=" N GLU D 882 " --> pdb=" O PRO D 878 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU D 887 " --> pdb=" O ALA D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 925 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.570A pdb=" N GLY A 157 " --> pdb=" O LEU A 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 185 Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 587 removed outlier: 3.621A pdb=" N VAL A 585 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 895 through 896 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.570A pdb=" N GLY B 157 " --> pdb=" O LEU B 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 185 Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AA9, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.622A pdb=" N VAL B 585 " --> pdb=" O VAL B 630 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 895 through 896 Processing sheet with id=AB2, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.570A pdb=" N GLY C 157 " --> pdb=" O LEU C 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 183 through 185 Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AB5, first strand: chain 'C' and resid 585 through 587 removed outlier: 3.623A pdb=" N VAL C 585 " --> pdb=" O VAL C 630 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 895 through 896 Processing sheet with id=AB7, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.569A pdb=" N GLY D 157 " --> pdb=" O LEU D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 183 through 185 Processing sheet with id=AB9, first strand: chain 'D' and resid 221 through 223 Processing sheet with id=AC1, first strand: chain 'D' and resid 585 through 587 removed outlier: 3.622A pdb=" N VAL D 585 " --> pdb=" O VAL D 630 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 895 through 896 764 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 11.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4137 1.30 - 1.43: 6167 1.43 - 1.56: 14069 1.56 - 1.68: 51 1.68 - 1.81: 148 Bond restraints: 24572 Sorted by residual: bond pdb=" CA GLN D 528 " pdb=" C GLN D 528 " ideal model delta sigma weight residual 1.522 1.441 0.081 1.40e-02 5.10e+03 3.36e+01 bond pdb=" CA GLN A 528 " pdb=" C GLN A 528 " ideal model delta sigma weight residual 1.522 1.441 0.081 1.40e-02 5.10e+03 3.34e+01 bond pdb=" CA GLN B 528 " pdb=" C GLN B 528 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.40e-02 5.10e+03 3.28e+01 bond pdb=" CA GLN C 528 " pdb=" C GLN C 528 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" C ILE C 584 " pdb=" N VAL C 585 " ideal model delta sigma weight residual 1.329 1.256 0.074 1.32e-02 5.74e+03 3.13e+01 ... (remaining 24567 not shown) Histogram of bond angle deviations from ideal: 91.36 - 102.84: 265 102.84 - 114.31: 14557 114.31 - 125.79: 17806 125.79 - 137.27: 812 137.27 - 148.74: 8 Bond angle restraints: 33448 Sorted by residual: angle pdb=" N LEU D 774 " pdb=" CA LEU D 774 " pdb=" C LEU D 774 " ideal model delta sigma weight residual 111.28 125.99 -14.71 1.35e+00 5.49e-01 1.19e+02 angle pdb=" N LEU C 774 " pdb=" CA LEU C 774 " pdb=" C LEU C 774 " ideal model delta sigma weight residual 111.28 125.98 -14.70 1.35e+00 5.49e-01 1.19e+02 angle pdb=" N LEU A 774 " pdb=" CA LEU A 774 " pdb=" C LEU A 774 " ideal model delta sigma weight residual 111.28 125.96 -14.68 1.35e+00 5.49e-01 1.18e+02 angle pdb=" N LEU B 774 " pdb=" CA LEU B 774 " pdb=" C LEU B 774 " ideal model delta sigma weight residual 111.28 125.94 -14.66 1.35e+00 5.49e-01 1.18e+02 angle pdb=" N LEU C 804 " pdb=" CA LEU C 804 " pdb=" C LEU C 804 " ideal model delta sigma weight residual 112.68 126.90 -14.22 1.33e+00 5.65e-01 1.14e+02 ... (remaining 33443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 12509 14.89 - 29.79: 1583 29.79 - 44.68: 448 44.68 - 59.57: 108 59.57 - 74.47: 36 Dihedral angle restraints: 14684 sinusoidal: 5380 harmonic: 9304 Sorted by residual: dihedral pdb=" CA ARG C 931 " pdb=" C ARG C 931 " pdb=" N ALA C 932 " pdb=" CA ALA C 932 " ideal model delta harmonic sigma weight residual 180.00 109.90 70.10 0 5.00e+00 4.00e-02 1.97e+02 dihedral pdb=" CA ARG A 931 " pdb=" C ARG A 931 " pdb=" N ALA A 932 " pdb=" CA ALA A 932 " ideal model delta harmonic sigma weight residual 180.00 109.93 70.07 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" CA ARG D 931 " pdb=" C ARG D 931 " pdb=" N ALA D 932 " pdb=" CA ALA D 932 " ideal model delta harmonic sigma weight residual 180.00 109.95 70.05 0 5.00e+00 4.00e-02 1.96e+02 ... (remaining 14681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3232 0.122 - 0.243: 454 0.243 - 0.365: 94 0.365 - 0.486: 20 0.486 - 0.608: 12 Chirality restraints: 3812 Sorted by residual: chirality pdb=" CG LEU C 804 " pdb=" CB LEU C 804 " pdb=" CD1 LEU C 804 " pdb=" CD2 LEU C 804 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" CG LEU D 804 " pdb=" CB LEU D 804 " pdb=" CD1 LEU D 804 " pdb=" CD2 LEU D 804 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.17e+00 chirality pdb=" CG LEU A 804 " pdb=" CB LEU A 804 " pdb=" CD1 LEU A 804 " pdb=" CD2 LEU A 804 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.16e+00 ... (remaining 3809 not shown) Planarity restraints: 4340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 785 " 0.029 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C LEU C 785 " -0.102 2.00e-02 2.50e+03 pdb=" O LEU C 785 " 0.039 2.00e-02 2.50e+03 pdb=" N VAL C 786 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 785 " 0.029 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C LEU D 785 " -0.102 2.00e-02 2.50e+03 pdb=" O LEU D 785 " 0.039 2.00e-02 2.50e+03 pdb=" N VAL D 786 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 785 " -0.029 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C LEU B 785 " 0.102 2.00e-02 2.50e+03 pdb=" O LEU B 785 " -0.039 2.00e-02 2.50e+03 pdb=" N VAL B 786 " -0.034 2.00e-02 2.50e+03 ... (remaining 4337 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3756 2.74 - 3.28: 26513 3.28 - 3.82: 44715 3.82 - 4.36: 51400 4.36 - 4.90: 76329 Nonbonded interactions: 202713 Sorted by model distance: nonbonded pdb=" OH TYR A 580 " pdb=" O ASN C 929 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR C 806 " pdb=" OG1 THR C 808 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR B 806 " pdb=" OG1 THR B 808 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR D 806 " pdb=" OG1 THR D 808 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR A 806 " pdb=" OG1 THR A 808 " model vdw 2.211 2.440 ... (remaining 202708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 15312 2.51 5 N 4148 2.21 5 O 4496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.480 Check model and map are aligned: 0.380 Process input model: 63.030 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 : 0.016 0.131 24572 Z= 1.095 Angle : 2.257 26.499 33448 Z= 1.190 Chirality : 0.102 0.608 3812 Planarity : 0.014 0.113 4340 Dihedral : 15.297 74.465 8716 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 2.60 % Allowed : 27.32 % Favored : 70.07 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 3.80 % Twisted Proline : 15.22 % Twisted General : 8.32 % 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: -5.98 (0.11), residues: 3228 helix: -3.24 (0.11), residues: 1068 sheet: -2.32 (0.36), residues: 208 loop : -4.91 (0.10), residues: 1952 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 268 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 20 residues processed: 320 average time/residue: 0.4415 time to fit residues: 207.1827 Evaluate side-chains 190 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 2.965 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3247 time to fit residues: 14.3941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 253 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 189 optimal weight: 0.0030 chunk 294 optimal weight: 6.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN A 167 HIS A 168 HIS A 224 HIS ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 GLN A 803 HIS A 832 HIS A 914 GLN A 926 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 167 HIS B 168 HIS B 224 HIS ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN B 803 HIS B 828 ASN B 832 HIS ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN B 926 ASN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 167 HIS C 168 HIS C 224 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN C 803 HIS C 828 ASN C 832 HIS C 914 GLN C 926 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 167 HIS D 168 HIS D 224 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 GLN D 803 HIS D 828 ASN D 832 HIS ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 GLN D 926 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 24572 Z= 0.308 Angle : 1.385 22.041 33448 Z= 0.646 Chirality : 0.059 0.409 3812 Planarity : 0.009 0.101 4340 Dihedral : 12.218 56.843 3456 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 34.90 Ramachandran Plot: Outliers : 1.30 % Allowed : 23.51 % Favored : 75.19 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.33 % Twisted Proline : 10.87 % Twisted General : 3.77 % 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: -5.01 (0.13), residues: 3228 helix: -1.67 (0.15), residues: 1088 sheet: -2.87 (0.31), residues: 220 loop : -4.70 (0.11), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 269 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 283 average time/residue: 0.4092 time to fit residues: 175.1934 Evaluate side-chains 180 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2063 time to fit residues: 5.4698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 244 optimal weight: 0.0570 chunk 200 optimal weight: 7.9990 chunk 81 optimal weight: 40.0000 chunk 294 optimal weight: 0.0010 chunk 318 optimal weight: 2.9990 chunk 262 optimal weight: 30.0000 chunk 292 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 236 optimal weight: 0.6980 overall best weight: 1.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 24572 Z= 0.268 Angle : 1.300 23.079 33448 Z= 0.597 Chirality : 0.056 0.343 3812 Planarity : 0.008 0.107 4340 Dihedral : 10.989 50.601 3456 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 31.14 Ramachandran Plot: Outliers : 0.74 % Allowed : 23.85 % Favored : 75.40 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.59 % Twisted Proline : 8.70 % Twisted General : 2.62 % 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: -4.42 (0.14), residues: 3228 helix: -0.82 (0.16), residues: 1068 sheet: -2.24 (0.35), residues: 212 loop : -4.59 (0.11), residues: 1948 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 255 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 263 average time/residue: 0.4047 time to fit residues: 161.5507 Evaluate side-chains 182 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2169 time to fit residues: 5.0483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 197 optimal weight: 20.0000 chunk 295 optimal weight: 0.3980 chunk 313 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 280 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 310 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN B 310 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN C 310 GLN ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN D 310 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 627 GLN ** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 24572 Z= 0.257 Angle : 1.269 21.875 33448 Z= 0.577 Chirality : 0.055 0.253 3812 Planarity : 0.008 0.111 4340 Dihedral : 10.077 47.257 3456 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 30.61 Ramachandran Plot: Outliers : 0.62 % Allowed : 21.96 % Favored : 77.42 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.59 % Twisted Proline : 6.52 % Twisted General : 2.33 % 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: -4.17 (0.14), residues: 3228 helix: -0.41 (0.17), residues: 1044 sheet: -2.29 (0.34), residues: 228 loop : -4.52 (0.11), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 251 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 254 average time/residue: 0.4219 time to fit residues: 161.9427 Evaluate side-chains 184 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 216 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 159 optimal weight: 0.2980 chunk 281 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 GLN ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 24572 Z= 0.252 Angle : 1.234 23.560 33448 Z= 0.559 Chirality : 0.054 0.316 3812 Planarity : 0.007 0.106 4340 Dihedral : 9.545 45.827 3456 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 29.53 Ramachandran Plot: Outliers : 0.62 % Allowed : 23.48 % Favored : 75.90 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.59 % Twisted Proline : 6.52 % Twisted General : 1.74 % 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: -4.05 (0.14), residues: 3228 helix: -0.21 (0.17), residues: 1044 sheet: -2.26 (0.34), residues: 228 loop : -4.50 (0.11), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 258 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 262 average time/residue: 0.3781 time to fit residues: 155.5274 Evaluate side-chains 188 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 183 optimal weight: 50.0000 chunk 77 optimal weight: 10.0000 chunk 313 optimal weight: 0.7980 chunk 260 optimal weight: 0.6980 chunk 145 optimal weight: 0.0470 chunk 26 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 ASN ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 24572 Z= 0.265 Angle : 1.227 23.271 33448 Z= 0.556 Chirality : 0.055 0.428 3812 Planarity : 0.007 0.096 4340 Dihedral : 9.327 47.855 3456 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 31.44 Ramachandran Plot: Outliers : 0.65 % Allowed : 23.27 % Favored : 76.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.69 % Twisted Proline : 6.52 % Twisted General : 1.61 % 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: -3.96 (0.14), residues: 3228 helix: -0.00 (0.17), residues: 1040 sheet: -2.28 (0.34), residues: 228 loop : -4.50 (0.11), residues: 1960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3544 time to fit residues: 131.4882 Evaluate side-chains 181 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.877 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 312 optimal weight: 3.9990 chunk 195 optimal weight: 30.0000 chunk 190 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 GLN ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN B 108 ASN B 146 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN C 146 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 ASN D 108 ASN D 146 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 HIS ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 24572 Z= 0.409 Angle : 1.313 25.971 33448 Z= 0.612 Chirality : 0.060 0.473 3812 Planarity : 0.008 0.093 4340 Dihedral : 9.768 45.799 3456 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 42.88 Ramachandran Plot: Outliers : 0.68 % Allowed : 25.93 % Favored : 73.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.69 % Twisted Proline : 6.52 % Twisted General : 1.83 % 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: -4.30 (0.14), residues: 3228 helix: -0.45 (0.16), residues: 1040 sheet: -3.17 (0.29), residues: 252 loop : -4.52 (0.12), residues: 1936 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3730 time to fit residues: 131.3754 Evaluate side-chains 168 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 20.0000 chunk 124 optimal weight: 0.4980 chunk 186 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 782 GLN ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 24572 Z= 0.288 Angle : 1.265 24.973 33448 Z= 0.579 Chirality : 0.058 0.425 3812 Planarity : 0.007 0.091 4340 Dihedral : 9.406 44.350 3456 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 35.87 Ramachandran Plot: Outliers : 0.62 % Allowed : 23.54 % Favored : 75.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.72 % Twisted Proline : 6.52 % Twisted General : 1.70 % 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: -4.11 (0.14), residues: 3228 helix: 0.07 (0.17), residues: 988 sheet: -2.83 (0.31), residues: 228 loop : -4.54 (0.11), residues: 2012 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3635 time to fit residues: 131.5424 Evaluate side-chains 171 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 3.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 291 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 89 optimal weight: 0.0020 chunk 262 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 289 optimal weight: 0.9980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 24572 Z= 0.257 Angle : 1.242 23.897 33448 Z= 0.561 Chirality : 0.057 0.426 3812 Planarity : 0.007 0.084 4340 Dihedral : 8.994 44.679 3456 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 32.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 22.77 % Favored : 76.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.72 % Twisted Proline : 5.98 % Twisted General : 1.21 % 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: -3.90 (0.14), residues: 3228 helix: 0.35 (0.18), residues: 980 sheet: -2.08 (0.34), residues: 208 loop : -4.53 (0.11), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3454 time to fit residues: 124.1998 Evaluate side-chains 163 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 322 optimal weight: 4.9990 chunk 297 optimal weight: 0.0170 chunk 257 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 GLN ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 24572 Z= 0.275 Angle : 1.238 23.821 33448 Z= 0.561 Chirality : 0.057 0.385 3812 Planarity : 0.007 0.080 4340 Dihedral : 8.915 43.552 3456 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 34.77 Ramachandran Plot: Outliers : 0.53 % Allowed : 23.30 % Favored : 76.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.72 % Twisted Proline : 6.52 % Twisted General : 1.11 % 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: -3.88 (0.14), residues: 3228 helix: 0.47 (0.18), residues: 976 sheet: -2.07 (0.34), residues: 208 loop : -4.57 (0.11), residues: 2044 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3514 time to fit residues: 122.3747 Evaluate side-chains 164 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.977 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 37 optimal weight: 0.0370 chunk 71 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 264 optimal weight: 40.0000 chunk 32 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 GLN ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.101081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.069831 restraints weight = 82406.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.067956 restraints weight = 82346.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.067686 restraints weight = 92441.992| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.6931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 24572 Z= 0.311 Angle : 1.238 24.658 33448 Z= 0.565 Chirality : 0.058 0.377 3812 Planarity : 0.007 0.077 4340 Dihedral : 8.943 43.183 3456 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 36.43 Ramachandran Plot: Outliers : 0.62 % Allowed : 24.04 % Favored : 75.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.72 % Twisted Proline : 6.52 % Twisted General : 1.25 % 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: -3.96 (0.14), residues: 3228 helix: 0.44 (0.18), residues: 976 sheet: -1.56 (0.38), residues: 164 loop : -4.66 (0.11), residues: 2088 =============================================================================== Job complete usr+sys time: 4034.89 seconds wall clock time: 75 minutes 51.71 seconds (4551.71 seconds total)