Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 23:06:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/04_2023/5yys_6859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/04_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_6859/04_2023/5yys_6859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/04_2023/5yys_6859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/04_2023/5yys_6859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/04_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 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 12.23, per 1000 atoms: 0.51 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: 9.79 Conformation dependent library (CDL) restraints added in 3.6 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: 1.05 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: 7.23 Time building geometry restraints manager: 10.45 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 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: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.030 Check model and map are aligned: 0.330 Set scattering table: 0.260 Process input model: 58.140 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 2.273 26.499 33448 Z= 1.217 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 : 2.711 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 20 residues processed: 320 average time/residue: 0.4387 time to fit residues: 205.7900 Evaluate side-chains 190 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3266 time to fit residues: 14.2226 ------------------------------------------------------------------------------- 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: 0.9990 chunk 83 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 253 optimal weight: 0.2980 chunk 98 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 189 optimal weight: 0.0030 chunk 294 optimal weight: 3.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- 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 ** 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 ** 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 832 HIS 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 ** 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 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 ** 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 832 HIS D 914 GLN D 926 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 24572 Z= 0.296 Angle : 1.285 16.129 33448 Z= 0.652 Chirality : 0.061 0.392 3812 Planarity : 0.009 0.101 4340 Dihedral : 12.254 56.257 3456 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 33.73 Ramachandran Plot: Outliers : 1.30 % Allowed : 22.74 % Favored : 75.96 % Rotamer Outliers : 0.50 % 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: -4.96 (0.13), residues: 3228 helix: -1.58 (0.15), residues: 1084 sheet: -2.87 (0.31), residues: 220 loop : -4.70 (0.11), residues: 1924 *********************** 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 305 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 293 time to evaluate : 2.803 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 outliers start: 12 outliers final: 4 residues processed: 305 average time/residue: 0.4060 time to fit residues: 185.3361 Evaluate side-chains 198 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1999 time to fit residues: 5.0778 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 200 optimal weight: 0.0980 chunk 81 optimal weight: 40.0000 chunk 294 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 292 optimal weight: 0.8980 chunk 100 optimal weight: 40.0000 chunk 236 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ** A 570 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 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN ** 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 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 24572 Z= 0.275 Angle : 1.187 15.648 33448 Z= 0.604 Chirality : 0.058 0.318 3812 Planarity : 0.008 0.109 4340 Dihedral : 10.994 50.633 3456 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 30.30 Ramachandran Plot: Outliers : 0.87 % Allowed : 23.64 % Favored : 75.50 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.33 % Twisted Proline : 6.52 % 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: -4.37 (0.14), residues: 3228 helix: -0.80 (0.16), residues: 1060 sheet: -2.17 (0.35), residues: 212 loop : -4.54 (0.12), residues: 1956 *********************** 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 264 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 252 time to evaluate : 2.850 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: 12 outliers final: 2 residues processed: 264 average time/residue: 0.3936 time to fit residues: 159.9248 Evaluate side-chains 183 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2296 time to fit residues: 4.8407 ------------------------------------------------------------------------------- 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: 0.9990 chunk 221 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 197 optimal weight: 0.0270 chunk 295 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 280 optimal weight: 0.0270 chunk 84 optimal weight: 20.0000 overall best weight: 1.0102 ------------------------------------------------------------------------------- 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 627 GLN A 745 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** B 310 GLN ** 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 851 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN ** C 310 GLN ** 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 851 GLN ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN ** D 310 GLN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 24572 Z= 0.264 Angle : 1.135 15.633 33448 Z= 0.580 Chirality : 0.057 0.296 3812 Planarity : 0.007 0.111 4340 Dihedral : 10.059 46.542 3456 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 31.23 Ramachandran Plot: Outliers : 0.74 % Allowed : 21.53 % Favored : 77.73 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.36 % Twisted Proline : 6.52 % Twisted General : 2.42 % 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: -4.07 (0.14), residues: 3228 helix: -0.31 (0.17), residues: 1036 sheet: -1.53 (0.37), residues: 204 loop : -4.52 (0.11), residues: 1988 *********************** 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 262 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 253 time to evaluate : 2.758 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: 9 outliers final: 0 residues processed: 262 average time/residue: 0.3698 time to fit residues: 153.3262 Evaluate side-chains 190 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9469 ------------------------------------------------------------------------------- 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: 9.9990 chunk 177 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 267 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 159 optimal weight: 4.9990 chunk 281 optimal weight: 30.0000 chunk 79 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 331 HIS ** 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** A 877 ASN ** B 104 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 745 GLN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 GLN ** 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 745 GLN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN C 877 ASN ** D 104 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 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: 0.6924 moved from start: 0.5624 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= 0.303 Angle : 1.153 13.644 33448 Z= 0.590 Chirality : 0.058 0.347 3812 Planarity : 0.007 0.113 4340 Dihedral : 9.891 49.692 3456 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 34.54 Ramachandran Plot: Outliers : 0.62 % Allowed : 23.54 % Favored : 75.84 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.46 % Twisted Proline : 6.52 % Twisted General : 2.06 % 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: -0.36 (0.17), residues: 1060 sheet: -2.72 (0.31), residues: 260 loop : -4.45 (0.12), residues: 1908 *********************** 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 233 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 229 time to evaluate : 2.979 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: 4 outliers final: 0 residues processed: 233 average time/residue: 0.3417 time to fit residues: 130.0074 Evaluate side-chains 167 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7936 ------------------------------------------------------------------------------- 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: 1.9990 chunk 282 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 183 optimal weight: 40.0000 chunk 77 optimal weight: 9.9990 chunk 313 optimal weight: 0.9990 chunk 260 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** 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 108 ASN B 146 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** 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 782 GLN ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 745 GLN ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 24572 Z= 0.358 Angle : 1.172 12.447 33448 Z= 0.602 Chirality : 0.060 0.472 3812 Planarity : 0.008 0.111 4340 Dihedral : 9.907 46.855 3456 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 38.89 Ramachandran Plot: Outliers : 0.62 % Allowed : 24.69 % Favored : 74.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.42 % Twisted Proline : 6.52 % Twisted General : 2.13 % 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: -4.15 (0.14), residues: 3228 helix: -0.40 (0.17), residues: 1056 sheet: -1.92 (0.34), residues: 204 loop : -4.56 (0.11), residues: 1968 *********************** 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 221 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 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 outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3287 time to fit residues: 119.9404 Evaluate side-chains 163 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7965 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 9.9990 chunk 178 optimal weight: 40.0000 chunk 228 optimal weight: 0.0980 chunk 177 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 175 optimal weight: 40.0000 chunk 312 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 190 optimal weight: 0.1980 chunk 144 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 570 ASN ** 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 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** D 108 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 763 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 24572 Z= 0.311 Angle : 1.148 12.515 33448 Z= 0.588 Chirality : 0.059 0.328 3812 Planarity : 0.007 0.113 4340 Dihedral : 9.665 50.638 3456 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 36.55 Ramachandran Plot: Outliers : 0.62 % Allowed : 24.41 % Favored : 74.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.52 % 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: -4.13 (0.14), residues: 3228 helix: -0.27 (0.17), residues: 1040 sheet: -2.46 (0.31), residues: 228 loop : -4.52 (0.11), residues: 1960 *********************** 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 227 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.900 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: 227 average time/residue: 0.3413 time to fit residues: 125.5706 Evaluate side-chains 162 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.759 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8030 ------------------------------------------------------------------------------- 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: 1.9990 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 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 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** 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 108 ASN ** 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 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 763 GLN ** 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: 0.6883 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 24572 Z= 0.280 Angle : 1.134 12.481 33448 Z= 0.578 Chirality : 0.060 0.434 3812 Planarity : 0.007 0.114 4340 Dihedral : 9.366 47.265 3456 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 34.35 Ramachandran Plot: Outliers : 0.53 % Allowed : 23.95 % Favored : 75.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.59 % Twisted Proline : 6.52 % Twisted General : 1.47 % 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: -4.01 (0.14), residues: 3228 helix: 0.03 (0.18), residues: 1016 sheet: -1.91 (0.34), residues: 204 loop : -4.57 (0.11), residues: 2008 *********************** 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 229 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.803 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: 229 average time/residue: 0.3506 time to fit residues: 130.3084 Evaluate side-chains 175 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9437 ------------------------------------------------------------------------------- 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: 5.9990 chunk 299 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 89 optimal weight: 40.0000 chunk 262 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 289 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 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 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 775 GLN ** 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 108 ASN ** 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 775 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 108 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** 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: 0.7026 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 24572 Z= 0.362 Angle : 1.179 13.157 33448 Z= 0.603 Chirality : 0.061 0.380 3812 Planarity : 0.008 0.114 4340 Dihedral : 9.578 47.323 3456 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 42.39 Ramachandran Plot: Outliers : 0.62 % Allowed : 25.71 % Favored : 73.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.46 % 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: -4.21 (0.14), residues: 3228 helix: -0.12 (0.17), residues: 1008 sheet: -2.29 (0.33), residues: 204 loop : -4.65 (0.11), residues: 2016 *********************** 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 212 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.166 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 outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3230 time to fit residues: 113.8139 Evaluate side-chains 161 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.574 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5647 ------------------------------------------------------------------------------- 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: 0.9980 chunk 307 optimal weight: 0.8980 chunk 187 optimal weight: 20.0000 chunk 145 optimal weight: 0.4980 chunk 213 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 297 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 763 GLN ** 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 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** 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 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 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 763 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.6863 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= 0.280 Angle : 1.143 13.611 33448 Z= 0.579 Chirality : 0.060 0.424 3812 Planarity : 0.007 0.113 4340 Dihedral : 9.218 45.395 3456 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 35.39 Ramachandran Plot: Outliers : 0.53 % Allowed : 23.64 % Favored : 75.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.52 % Twisted Proline : 6.52 % Twisted General : 1.41 % 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: -4.00 (0.14), residues: 3228 helix: 0.10 (0.18), residues: 1016 sheet: -0.95 (0.40), residues: 144 loop : -4.63 (0.11), residues: 2068 ********************** 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 220 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.979 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 outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3467 time to fit residues: 125.7172 Evaluate side-chains 159 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6878 ------------------------------------------------------------------------------- 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: 6.9990 chunk 273 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 237 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 71 optimal weight: 0.9990 chunk 257 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 chunk 32 optimal weight: 40.0000 chunk 47 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS ** 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 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** 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 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** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 ASN ** D 763 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.105018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3890 r_free = 0.3890 target = 0.073972 restraints weight = 78560.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.071900 restraints weight = 85658.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.071334 restraints weight = 110251.161| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.7313 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= 0.266 Angle : 1.116 13.133 33448 Z= 0.564 Chirality : 0.059 0.390 3812 Planarity : 0.007 0.112 4340 Dihedral : 8.904 45.217 3456 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 33.37 Ramachandran Plot: Outliers : 0.53 % Allowed : 24.16 % Favored : 75.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.59 % Twisted Proline : 5.98 % 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: -3.90 (0.14), residues: 3228 helix: 0.27 (0.18), residues: 1008 sheet: -1.24 (0.39), residues: 168 loop : -4.61 (0.11), residues: 2052 =============================================================================== Job complete usr+sys time: 3981.14 seconds wall clock time: 74 minutes 40.40 seconds (4480.40 seconds total)