Starting phenix.real_space_refine on Thu Aug 8 20:41:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/08_2024/5yys_6859.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/08_2024/5yys_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_6859/08_2024/5yys_6859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/08_2024/5yys_6859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/08_2024/5yys_6859.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/08_2024/5yys_6859.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 12.96, per 1000 atoms: 0.54 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: 9.57 Conformation dependent library (CDL) restraints added in 4.1 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: 2.56 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: 7.06 Time building geometry restraints manager: 10.48 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 3.040 nonbonded pdb=" OH TYR C 806 " pdb=" OG1 THR C 808 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR B 806 " pdb=" OG1 THR B 808 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR D 806 " pdb=" OG1 THR D 808 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR A 806 " pdb=" OG1 THR A 808 " model vdw 2.211 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.680 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: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 62.520 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.040 ------------------------------------------------------------------------------- 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 % Allowed : 9.68 % Favored : 87.98 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.007 TRP C 336 HIS 0.022 0.005 HIS B 842 PHE 0.063 0.007 PHE B 654 TYR 0.048 0.008 TYR A 891 ARG 0.018 0.002 ARG D 948 *********************** 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 : 2.670 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: A 579 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7909 (t) REVERT: A 595 MET cc_start: 0.6627 (mmt) cc_final: 0.6351 (mmt) REVERT: A 741 ASN cc_start: 0.9526 (m-40) cc_final: 0.9176 (m-40) REVERT: B 108 ASN cc_start: 0.9261 (m-40) cc_final: 0.8787 (t0) REVERT: B 579 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7930 (t) REVERT: B 595 MET cc_start: 0.6802 (mmt) cc_final: 0.6442 (mmt) REVERT: B 741 ASN cc_start: 0.9380 (m-40) cc_final: 0.9043 (m-40) REVERT: C 579 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7866 (t) REVERT: C 595 MET cc_start: 0.6755 (mmt) cc_final: 0.6435 (mmt) REVERT: C 741 ASN cc_start: 0.9401 (m-40) cc_final: 0.9073 (m-40) REVERT: D 108 ASN cc_start: 0.9279 (m-40) cc_final: 0.8889 (t0) REVERT: D 579 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7776 (t) REVERT: D 595 MET cc_start: 0.6798 (mmt) cc_final: 0.6474 (mmt) REVERT: D 741 ASN cc_start: 0.9407 (m-40) cc_final: 0.9080 (m-40) outliers start: 56 outliers final: 20 residues processed: 320 average time/residue: 0.4442 time to fit residues: 210.9053 Evaluate side-chains 199 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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: 6.9990 chunk 245 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 253 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** 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 745 GLN A 763 GLN A 782 GLN A 803 HIS A 828 ASN 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 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN 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 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 763 GLN 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 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 GLN 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: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3250 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= 0.322 Angle : 1.317 16.366 33448 Z= 0.671 Chirality : 0.063 0.403 3812 Planarity : 0.009 0.094 4340 Dihedral : 12.390 55.846 3456 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 30.76 Ramachandran Plot: Outliers : 1.21 % Allowed : 23.30 % Favored : 75.50 % Rotamer: Outliers : 0.67 % Allowed : 6.34 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.33 % Twisted Proline : 10.87 % Twisted General : 4.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.12), residues: 3228 helix: -1.73 (0.14), residues: 1088 sheet: -2.44 (0.34), residues: 160 loop : -4.68 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 336 HIS 0.007 0.002 HIS A 129 PHE 0.035 0.002 PHE A 654 TYR 0.031 0.003 TYR C 891 ARG 0.005 0.001 ARG B 101 *********************** 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 298 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 282 time to evaluate : 2.770 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7538 (t) REVERT: A 608 TYR cc_start: 0.8444 (t80) cc_final: 0.8017 (t80) REVERT: B 232 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6140 (tptt) REVERT: B 579 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7312 (t) REVERT: C 232 LYS cc_start: 0.7457 (mmtt) cc_final: 0.6144 (tptt) REVERT: C 579 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7241 (t) REVERT: D 232 LYS cc_start: 0.7541 (mmtt) cc_final: 0.6239 (tptt) REVERT: D 579 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6959 (t) outliers start: 16 outliers final: 4 residues processed: 298 average time/residue: 0.4106 time to fit residues: 184.7301 Evaluate side-chains 197 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 2.484 ------------------------------------------------------------------------------- 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: 6.9990 chunk 91 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 81 optimal weight: 50.0000 chunk 294 optimal weight: 4.9990 chunk 318 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 100 optimal weight: 40.0000 chunk 236 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN ** 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 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 ** 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 612 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 ** 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 745 GLN ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24572 Z= 0.368 Angle : 1.271 13.989 33448 Z= 0.652 Chirality : 0.062 0.394 3812 Planarity : 0.009 0.107 4340 Dihedral : 11.619 52.882 3456 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 35.54 Ramachandran Plot: Outliers : 0.99 % Allowed : 24.85 % Favored : 74.16 % Rotamer: Outliers : 0.21 % Allowed : 7.30 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.33 % Twisted Proline : 8.15 % Twisted General : 2.98 % 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: -4.67 (0.13), residues: 3228 helix: -1.26 (0.16), residues: 1092 sheet: -2.44 (0.31), residues: 212 loop : -4.62 (0.11), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 336 HIS 0.007 0.002 HIS D 796 PHE 0.033 0.002 PHE A 654 TYR 0.030 0.003 TYR A 138 ARG 0.006 0.001 ARG B 852 *********************** 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 225 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 220 time to evaluate : 2.490 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: A 232 LYS cc_start: 0.6975 (mmtt) cc_final: 0.5779 (tptt) REVERT: B 232 LYS cc_start: 0.7391 (mmtt) cc_final: 0.6133 (tptt) REVERT: C 232 LYS cc_start: 0.7473 (mmtt) cc_final: 0.6184 (tptt) REVERT: C 648 MET cc_start: 0.6929 (mtt) cc_final: 0.6439 (mtt) REVERT: D 232 LYS cc_start: 0.7506 (mmtt) cc_final: 0.6239 (tptt) REVERT: D 648 MET cc_start: 0.6669 (mtt) cc_final: 0.6400 (mtt) outliers start: 5 outliers final: 4 residues processed: 225 average time/residue: 0.3834 time to fit residues: 132.1637 Evaluate side-chains 174 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 2.534 ------------------------------------------------------------------------------- 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: 3.9990 chunk 221 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 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 ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** 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 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 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 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: 0.6991 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24572 Z= 0.306 Angle : 1.212 12.797 33448 Z= 0.621 Chirality : 0.061 0.379 3812 Planarity : 0.008 0.101 4340 Dihedral : 10.902 49.977 3456 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 31.27 Ramachandran Plot: Outliers : 0.71 % Allowed : 23.27 % Favored : 76.02 % Rotamer: Outliers : 0.33 % Allowed : 5.76 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.46 % Twisted Proline : 8.15 % Twisted General : 2.69 % 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: -4.46 (0.13), residues: 3228 helix: -0.89 (0.16), residues: 1092 sheet: -1.86 (0.36), residues: 180 loop : -4.66 (0.11), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 599 HIS 0.007 0.001 HIS B 796 PHE 0.027 0.002 PHE A 654 TYR 0.025 0.002 TYR A 138 ARG 0.004 0.001 ARG A 571 *********************** 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 248 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 240 time to evaluate : 2.836 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LYS cc_start: 0.7195 (mmtt) cc_final: 0.5953 (tptt) REVERT: B 232 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6263 (tptt) REVERT: B 648 MET cc_start: 0.7084 (mmt) cc_final: 0.6877 (mmt) REVERT: B 804 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6427 (pp) REVERT: B 846 MET cc_start: 0.9147 (tpp) cc_final: 0.8835 (tpp) REVERT: C 232 LYS cc_start: 0.7339 (mmtt) cc_final: 0.6246 (tptt) REVERT: C 804 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6476 (pp) REVERT: C 846 MET cc_start: 0.9140 (tpp) cc_final: 0.8934 (tpp) REVERT: D 232 LYS cc_start: 0.7417 (mmtt) cc_final: 0.6349 (tptt) REVERT: D 804 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6260 (pp) REVERT: D 846 MET cc_start: 0.9200 (tpp) cc_final: 0.8878 (tpp) outliers start: 8 outliers final: 0 residues processed: 248 average time/residue: 0.3864 time to fit residues: 146.4125 Evaluate side-chains 195 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 0.0570 chunk 267 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 159 optimal weight: 3.9990 chunk 281 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** 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 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** 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 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5252 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= 0.300 Angle : 1.192 12.878 33448 Z= 0.611 Chirality : 0.061 0.428 3812 Planarity : 0.008 0.093 4340 Dihedral : 10.441 52.768 3456 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 30.42 Ramachandran Plot: Outliers : 0.65 % Allowed : 23.39 % Favored : 75.96 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.46 % Twisted Proline : 6.52 % Twisted General : 2.49 % 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: -4.41 (0.13), residues: 3228 helix: -0.63 (0.17), residues: 1064 sheet: -2.30 (0.37), residues: 168 loop : -4.65 (0.11), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 599 HIS 0.007 0.001 HIS D 637 PHE 0.030 0.002 PHE C 654 TYR 0.024 0.002 TYR A 138 ARG 0.005 0.001 ARG C 140 *********************** 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 231 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.661 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: A 232 LYS cc_start: 0.7117 (mmtt) cc_final: 0.5936 (tptt) REVERT: A 616 LEU cc_start: 0.8463 (pp) cc_final: 0.8130 (pp) REVERT: A 846 MET cc_start: 0.9136 (mmt) cc_final: 0.8884 (mmt) REVERT: B 121 MET cc_start: 0.4776 (mtm) cc_final: 0.4550 (mpp) REVERT: B 232 LYS cc_start: 0.7415 (mmtt) cc_final: 0.6449 (tptt) REVERT: B 307 MET cc_start: 0.2230 (ppp) cc_final: 0.1938 (ttp) REVERT: B 616 LEU cc_start: 0.8390 (pp) cc_final: 0.8100 (pp) REVERT: B 792 HIS cc_start: 0.7922 (t-90) cc_final: 0.7685 (t70) REVERT: C 121 MET cc_start: 0.4765 (mtm) cc_final: 0.4559 (mpp) REVERT: C 232 LYS cc_start: 0.7450 (mmtt) cc_final: 0.6427 (tptt) REVERT: C 307 MET cc_start: 0.2192 (ppp) cc_final: 0.1909 (ttp) REVERT: C 792 HIS cc_start: 0.7930 (t-90) cc_final: 0.7694 (t70) REVERT: D 121 MET cc_start: 0.4788 (mtm) cc_final: 0.4562 (mpp) REVERT: D 232 LYS cc_start: 0.7508 (mmtt) cc_final: 0.6514 (tptt) REVERT: D 616 LEU cc_start: 0.8269 (pp) cc_final: 0.7948 (pp) REVERT: D 648 MET cc_start: 0.6790 (mtt) cc_final: 0.6352 (mtt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3745 time to fit residues: 133.2371 Evaluate side-chains 175 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.815 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 10.0000 chunk 183 optimal weight: 40.0000 chunk 77 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: