Starting phenix.real_space_refine on Tue Mar 19 11:10:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/03_2024/5yys_6859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/03_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_6859/03_2024/5yys_6859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/03_2024/5yys_6859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/03_2024/5yys_6859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yys_6859/03_2024/5yys_6859.pdb" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.20, 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: 10.31 Conformation dependent library (CDL) restraints added in 4.2 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: 2.41 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: 7.01 Time building geometry restraints manager: 11.16 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: 0.700 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: 4.280 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 61.940 Find NCS groups from input model: 1.650 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.050 ------------------------------------------------------------------------------- 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 : 2.430 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: 0.4315 time to fit residues: 202.9641 Evaluate side-chains 199 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 2.925 ------------------------------------------------------------------------------- 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: 6.9990 chunk 154 optimal weight: 4.9990 chunk 189 optimal weight: 0.0030 chunk 294 optimal weight: 2.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- 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: 0.6928 moved from start: 0.3354 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= 0.295 Angle : 1.280 15.035 33448 Z= 0.650 Chirality : 0.062 0.408 3812 Planarity : 0.009 0.101 4340 Dihedral : 12.121 55.099 3456 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 33.07 Ramachandran Plot: Outliers : 1.30 % Allowed : 22.61 % Favored : 76.08 % Rotamer: Outliers : 0.67 % Allowed : 5.84 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.33 % Twisted Proline : 10.87 % Twisted General : 3.41 % 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: -4.99 (0.13), residues: 3228 helix: -1.53 (0.15), residues: 1080 sheet: -2.89 (0.31), residues: 220 loop : -4.76 (0.11), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 336 HIS 0.008 0.002 HIS A 129 PHE 0.039 0.002 PHE A 654 TYR 0.032 0.003 TYR C 138 ARG 0.005 0.001 ARG D 918 *********************** 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 322 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 306 time to evaluate : 2.318 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: symmetry clash revert: symmetry clash REVERT: A 608 TYR cc_start: 0.8562 (t80) cc_final: 0.8176 (t80) REVERT: A 741 ASN cc_start: 0.9266 (m-40) cc_final: 0.8701 (p0) REVERT: B 232 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6155 (tptt) REVERT: B 608 TYR cc_start: 0.8249 (t80) cc_final: 0.7848 (t80) REVERT: B 741 ASN cc_start: 0.9039 (m-40) cc_final: 0.8558 (p0) REVERT: C 232 LYS cc_start: 0.7511 (mmtt) cc_final: 0.6224 (tptt) REVERT: C 608 TYR cc_start: 0.8318 (t80) cc_final: 0.7884 (t80) REVERT: C 741 ASN cc_start: 0.9027 (m-40) cc_final: 0.8565 (p0) REVERT: C 799 TYR cc_start: 0.6548 (m-80) cc_final: 0.6337 (p90) REVERT: D 232 LYS cc_start: 0.7534 (mmtt) cc_final: 0.6259 (tptt) REVERT: D 608 TYR cc_start: 0.8295 (t80) cc_final: 0.7881 (t80) REVERT: D 741 ASN cc_start: 0.9058 (m-40) cc_final: 0.8568 (p0) outliers start: 16 outliers final: 4 residues processed: 322 average time/residue: 0.4021 time to fit residues: 195.8544 Evaluate side-chains 206 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 202 time to evaluate : 3.071 ------------------------------------------------------------------------------- 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: 0.0040 chunk 91 optimal weight: 0.0970 chunk 244 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 81 optimal weight: 50.0000 chunk 294 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 262 optimal weight: 20.0000 chunk 292 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 GLN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** 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 ** 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** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** 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 ** 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 ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4681 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= 0.276 Angle : 1.184 15.850 33448 Z= 0.603 Chirality : 0.059 0.322 3812 Planarity : 0.008 0.110 4340 Dihedral : 10.854 49.921 3456 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 29.91 Ramachandran Plot: Outliers : 0.74 % Allowed : 23.23 % Favored : 76.02 % Rotamer: Outliers : 0.54 % Allowed : 6.22 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.19 % Twisted Proline : 6.52 % Twisted General : 2.79 % 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: -4.29 (0.14), residues: 3228 helix: -0.75 (0.16), residues: 1060 sheet: -1.53 (0.37), residues: 188 loop : -4.53 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 336 HIS 0.006 0.001 HIS B 129 PHE 0.035 0.002 PHE A 654 TYR 0.026 0.002 TYR A 138 ARG 0.004 0.001 ARG B 222 *********************** 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 291 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 278 time to evaluate : 2.596 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: A 232 LYS cc_start: 0.7539 (mmpt) cc_final: 0.6909 (tptt) REVERT: A 741 ASN cc_start: 0.9090 (m-40) cc_final: 0.8731 (p0) REVERT: B 232 LYS cc_start: 0.7576 (mmtt) cc_final: 0.6602 (tptt) REVERT: B 732 ASP cc_start: 0.8203 (t0) cc_final: 0.7989 (t0) REVERT: B 741 ASN cc_start: 0.8858 (m-40) cc_final: 0.8585 (p0) REVERT: C 232 LYS cc_start: 0.7639 (mmtt) cc_final: 0.6647 (tptt) REVERT: C 741 ASN cc_start: 0.8862 (m-40) cc_final: 0.8580 (p0) REVERT: C 804 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6792 (pp) REVERT: D 232 LYS cc_start: 0.7658 (mmtt) cc_final: 0.6679 (tptt) REVERT: D 741 ASN cc_start: 0.8866 (m-40) cc_final: 0.8601 (p0) outliers start: 13 outliers final: 1 residues processed: 291 average time/residue: 0.4030 time to fit residues: 176.3370 Evaluate side-chains 210 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 2.615 ------------------------------------------------------------------------------- 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: 0.0050 chunk 221 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 313 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 280 optimal weight: 0.1980 chunk 84 optimal weight: 20.0000 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 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 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 287 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 GLN ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24572 Z= 0.265 Angle : 1.148 15.529 33448 Z= 0.585 Chirality : 0.058 0.287 3812 Planarity : 0.007 0.114 4340 Dihedral : 10.102 47.658 3456 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.59 % Allowed : 21.69 % Favored : 77.73 % Rotamer: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.23 % Twisted Proline : 6.52 % Twisted General : 2.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.14), residues: 3228 helix: -0.25 (0.17), residues: 1040 sheet: -1.83 (0.33), residues: 244 loop : -4.54 (0.11), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 866 HIS 0.007 0.001 HIS B 129 PHE 0.037 0.002 PHE D 654 TYR 0.029 0.002 TYR A 138 ARG 0.003 0.000 ARG A 641 *********************** 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 261 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 257 time to evaluate : 2.929 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: A 232 LYS cc_start: 0.8055 (mmpt) cc_final: 0.7441 (tptt) REVERT: A 616 LEU cc_start: 0.8232 (pp) cc_final: 0.7742 (pp) REVERT: A 741 ASN cc_start: 0.9090 (m-40) cc_final: 0.8748 (p0) REVERT: B 232 LYS cc_start: 0.7381 (mmtt) cc_final: 0.6532 (tptt) REVERT: B 595 MET cc_start: 0.6700 (mmp) cc_final: 0.6389 (mmp) REVERT: B 741 ASN cc_start: 0.8798 (m-40) cc_final: 0.8530 (p0) REVERT: C 232 LYS cc_start: 0.7534 (mmtt) cc_final: 0.6688 (tptt) REVERT: C 616 LEU cc_start: 0.8215 (pp) cc_final: 0.7942 (pp) REVERT: C 648 MET cc_start: 0.7665 (mmm) cc_final: 0.7446 (mmm) REVERT: C 741 ASN cc_start: 0.8770 (m-40) cc_final: 0.8524 (p0) REVERT: C 804 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6430 (pp) REVERT: D 232 LYS cc_start: 0.7485 (mmtt) cc_final: 0.6602 (tptt) REVERT: D 595 MET cc_start: 0.6660 (mmp) cc_final: 0.6404 (mmp) REVERT: D 741 ASN cc_start: 0.8798 (m-40) cc_final: 0.8541 (p0) outliers start: 4 outliers final: 0 residues processed: 261 average time/residue: 0.3751 time to fit residues: 152.3813 Evaluate side-chains 207 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.740 ------------------------------------------------------------------------------- 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: 10.0000 chunk 177 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 216 optimal weight: 0.3980 chunk 0 optimal weight: 50.0000 chunk 159 optimal weight: 5.9990 chunk 281 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 ** 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** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.5544 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= 0.290 Angle : 1.146 13.569 33448 Z= 0.585 Chirality : 0.058 0.346 3812 Planarity : 0.007 0.107 4340 Dihedral : 9.813 45.981 3456 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 33.54 Ramachandran Plot: Outliers : 0.62 % Allowed : 23.30 % Favored : 76.08 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.33 % Twisted Proline : 6.52 % Twisted General : 1.87 % 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: -3.92 (0.14), residues: 3228 helix: -0.26 (0.17), residues: 1068 sheet: -1.50 (0.36), residues: 204 loop : -4.44 (0.12), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 866 HIS 0.006 0.001 HIS B 129 PHE 0.037 0.002 PHE A 654 TYR 0.028 0.002 TYR A 629 ARG 0.006 0.001 ARG B 641 *********************** 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 244 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.743 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: A 204 MET cc_start: 0.4140 (tpp) cc_final: 0.3882 (tpt) REVERT: A 232 LYS cc_start: 0.7825 (mmpt) cc_final: 0.7274 (tptt) REVERT: A 648 MET cc_start: 0.6955 (mmp) cc_final: 0.6564 (mmm) REVERT: A 741 ASN cc_start: 0.9165 (m-40) cc_final: 0.8738 (p0) REVERT: A 782 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8572 (tp40) REVERT: A 846 MET cc_start: 0.9034 (mmt) cc_final: 0.8703 (mmt) REVERT: B 232 LYS cc_start: 0.7213 (mmtt) cc_final: 0.6416 (tptt) REVERT: B 645 MET cc_start: 0.6686 (ppp) cc_final: 0.6455 (ppp) REVERT: B 741 ASN cc_start: 0.8912 (m-40) cc_final: 0.8568 (p0) REVERT: C 232 LYS cc_start: 0.7436 (mmtt) cc_final: 0.6632 (tptt) REVERT: C 616 LEU cc_start: 0.8207 (pp) cc_final: 0.7692 (pp) REVERT: C 648 MET cc_start: 0.7899 (mmm) cc_final: 0.7487 (mmm) REVERT: C 741 ASN cc_start: 0.8900 (m-40) cc_final: 0.8547 (p0) REVERT: D 232 LYS cc_start: 0.7371 (mmtt) cc_final: 0.6545 (tptt) REVERT: D 616 LEU cc_start: 0.8137 (pp) cc_final: 0.7816 (pp) REVERT: D 741 ASN cc_start: 0.8937 (m-40) cc_final: 0.8571 (p0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3974 time to fit residues: 153.6231 Evaluate side-chains 181 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.910 ------------------------------------------------------------------------------- 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: 2.9990 chunk 282 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 183 optimal weight: 0.0270 chunk 77 optimal weight: 6.9990 chunk 313 optimal weight: 0.9990 chunk 260 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 overall best weight: 2.1444 ------------------------------------------------------------------------------- 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 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 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN C 869 ASN ** 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** ** D 851 GLN ** 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: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24572 Z= 0.283 Angle : 1.130 12.390 33448 Z= 0.577 Chirality : 0.057 0.384 3812 Planarity : 0.007 0.112 4340 Dihedral : 9.567 49.951 3456 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 31.93 Ramachandran Plot: Outliers : 0.59 % Allowed : 22.49 % Favored : 76.92 % Rotamer: Outliers : 0.17 % Allowed : 4.30 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.33 % Twisted Proline : 6.52 % Twisted General : 1.87 % 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: -3.89 (0.14), residues: 3228 helix: -0.22 (0.17), residues: 1088 sheet: -1.67 (0.35), residues: 208 loop : -4.45 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 599 HIS 0.010 0.001 HIS D 129 PHE 0.031 0.002 PHE C 654 TYR 0.026 0.002 TYR D 891 ARG 0.004 0.000 ARG A 375 *********************** 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 235 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 2.922 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: A 232 LYS cc_start: 0.7781 (mmpt) cc_final: 0.7249 (tptt) REVERT: A 579 VAL cc_start: 0.6918 (OUTLIER) cc_final: 0.6649 (m) REVERT: A 645 MET cc_start: 0.6887 (ppp) cc_final: 0.6612 (ppp) REVERT: A 648 MET cc_start: 0.7156 (mmp) cc_final: 0.6817 (mmm) REVERT: A 741 ASN cc_start: 0.9200 (m-40) cc_final: 0.8711 (p0) REVERT: A 782 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8596 (tp40) REVERT: B 232 LYS cc_start: 0.7256 (mmtt) cc_final: 0.6474 (tptt) REVERT: B 579 VAL cc_start: 0.6617 (OUTLIER) cc_final: 0.6265 (m) REVERT: B 741 ASN cc_start: 0.8894 (m-40) cc_final: 0.8538 (p0) REVERT: C 232 LYS cc_start: 0.7527 (mmtt) cc_final: 0.6789 (tptt) REVERT: C 579 VAL cc_start: 0.6656 (OUTLIER) cc_final: 0.6188 (m) REVERT: C 616 LEU cc_start: 0.8073 (pp) cc_final: 0.7691 (pp) REVERT: C 645 MET cc_start: 0.6652 (ppp) cc_final: 0.6319 (ppp) REVERT: C 648 MET cc_start: 0.7966 (mmm) cc_final: 0.7558 (mmm) REVERT: C 741 ASN cc_start: 0.8891 (m-40) cc_final: 0.8524 (p0) REVERT: D 232 LYS cc_start: 0.7569 (mmtt) cc_final: 0.6823 (tptt) REVERT: D 579 VAL cc_start: 0.6484 (OUTLIER) cc_final: 0.5991 (m) REVERT: D 741 ASN cc_start: 0.8909 (m-40) cc_final: 0.8543 (p0) outliers start: 4 outliers final: 0 residues processed: 235 average time/residue: 0.3418 time to fit residues: 128.2184 Evaluate side-chains 191 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 2.551 ------------------------------------------------------------------------------- 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: 7.9990 chunk 35 optimal weight: 0.0070 chunk 178 optimal weight: 30.0000 chunk 228 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 263 optimal weight: 30.0000 chunk 175 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN ** A 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 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 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 842 HIS ** 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 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.6168 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= 0.277 Angle : 1.118 12.486 33448 Z= 0.571 Chirality : 0.059 0.429 3812 Planarity : 0.007 0.111 4340 Dihedral : 9.406 46.100 3456 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 31.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 24.23 % Favored : 75.28 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.46 % Twisted Proline : 6.52 % Twisted General : 1.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.14), residues: 3228 helix: -0.04 (0.17), residues: 1036 sheet: -1.71 (0.34), residues: 208 loop : -4.39 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 866 HIS 0.010 0.001 HIS D 129 PHE 0.028 0.002 PHE B 654 TYR 0.021 0.002 TYR A 660 ARG 0.004 0.000 ARG D 918 *********************** 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 237 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.782 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: A 232 LYS cc_start: 0.7841 (mmpt) cc_final: 0.7309 (tptt) REVERT: A 741 ASN cc_start: 0.9090 (m-40) cc_final: 0.8682 (p0) REVERT: B 232 LYS cc_start: 0.7437 (mmtt) cc_final: 0.6737 (tptt) REVERT: B 297 MET cc_start: 0.1150 (ptp) cc_final: 0.0882 (ptt) REVERT: B 616 LEU cc_start: 0.8155 (pp) cc_final: 0.7801 (pp) REVERT: B 741 ASN cc_start: 0.8897 (m-40) cc_final: 0.8537 (p0) REVERT: C 121 MET cc_start: 0.4424 (mpp) cc_final: 0.4141 (mpp) REVERT: C 232 LYS cc_start: 0.7503 (mmtt) cc_final: 0.6774 (tptt) REVERT: C 297 MET cc_start: 0.1132 (ptp) cc_final: 0.0878 (ptt) REVERT: C 616 LEU cc_start: 0.8120 (pp) cc_final: 0.7798 (pp) REVERT: C 741 ASN cc_start: 0.8895 (m-40) cc_final: 0.8527 (p0) REVERT: D 232 LYS cc_start: 0.7547 (mmtt) cc_final: 0.6809 (tptt) REVERT: D 297 MET cc_start: 0.1106 (ptp) cc_final: 0.0864 (ptt) REVERT: D 616 LEU cc_start: 0.7890 (pp) cc_final: 0.7598 (pp) REVERT: D 741 ASN cc_start: 0.8916 (m-40) cc_final: 0.8544 (p0) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3611 time to fit residues: 138.4250 Evaluate side-chains 191 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.835 ------------------------------------------------------------------------------- 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: 0.0370 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 154 optimal weight: 0.2980 chunk 29 optimal weight: 8.9990 chunk 245 optimal weight: 0.8980 overall best weight: 1.2462 ------------------------------------------------------------------------------- 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 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 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 796 HIS ** 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 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** 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 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24572 Z= 0.268 Angle : 1.129 12.721 33448 Z= 0.576 Chirality : 0.059 0.419 3812 Planarity : 0.007 0.116 4340 Dihedral : 9.182 51.741 3456 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 31.48 Ramachandran Plot: Outliers : 0.50 % Allowed : 22.49 % Favored : 77.01 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.46 % Twisted Proline : 6.52 % Twisted General : 1.44 % 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: -3.79 (0.14), residues: 3228 helix: 0.15 (0.17), residues: 1032 sheet: -1.69 (0.35), residues: 208 loop : -4.44 (0.11), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 866 HIS 0.011 0.001 HIS D 129 PHE 0.028 0.002 PHE A 654 TYR 0.027 0.002 TYR D 660 ARG 0.014 0.000 ARG B 787 *********************** 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 245 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.778 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: A 155 CYS cc_start: 0.8216 (m) cc_final: 0.7968 (t) REVERT: A 204 MET cc_start: 0.4190 (tpp) cc_final: 0.3707 (tpt) REVERT: A 232 LYS cc_start: 0.7680 (mmpt) cc_final: 0.7158 (tptt) REVERT: A 741 ASN cc_start: 0.9160 (m-40) cc_final: 0.8683 (p0) REVERT: B 232 LYS cc_start: 0.7281 (mmtt) cc_final: 0.6586 (tptt) REVERT: B 741 ASN cc_start: 0.8953 (m-40) cc_final: 0.8580 (p0) REVERT: C 121 MET cc_start: 0.4472 (mpp) cc_final: 0.4184 (mpp) REVERT: C 232 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6634 (tptt) REVERT: C 645 MET cc_start: 0.6683 (ppp) cc_final: 0.6240 (ppp) REVERT: C 741 ASN cc_start: 0.8931 (m-40) cc_final: 0.8555 (p0) REVERT: D 232 LYS cc_start: 0.7509 (mmtt) cc_final: 0.6790 (tptt) REVERT: D 645 MET cc_start: 0.6225 (ppp) cc_final: 0.5799 (ppp) REVERT: D 741 ASN cc_start: 0.8969 (m-40) cc_final: 0.8598 (p0) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3529 time to fit residues: 139.6614 Evaluate side-chains 188 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 chunk 291 optimal weight: 0.9980 chunk 175 optimal weight: 50.0000 chunk 126 optimal weight: 0.9980 chunk 228 optimal weight: 0.0040 chunk 89 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 289 optimal weight: 6.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** B 570 ASN ** 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 146 GLN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.6710 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= 0.296 Angle : 1.132 18.449 33448 Z= 0.577 Chirality : 0.060 0.426 3812 Planarity : 0.007 0.117 4340 Dihedral : 9.111 48.333 3456 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 35.34 Ramachandran Plot: Outliers : 0.50 % Allowed : 24.07 % Favored : 75.43 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.42 % Twisted Proline : 5.98 % Twisted General : 1.44 % 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: -3.87 (0.14), residues: 3228 helix: 0.13 (0.17), residues: 1008 sheet: -1.95 (0.32), residues: 256 loop : -4.48 (0.11), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 866 HIS 0.012 0.001 HIS C 129 PHE 0.035 0.002 PHE B 654 TYR 0.025 0.002 TYR A 138 ARG 0.009 0.000 ARG B 787 *********************** 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 233 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.672 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: A 155 CYS cc_start: 0.8207 (m) cc_final: 0.7935 (t) REVERT: A 204 MET cc_start: 0.4054 (tpp) cc_final: 0.3665 (tpt) REVERT: A 232 LYS cc_start: 0.7689 (mmpt) cc_final: 0.7153 (tptt) REVERT: A 645 MET cc_start: 0.6609 (ppp) cc_final: 0.6213 (ppp) REVERT: A 741 ASN cc_start: 0.9125 (m-40) cc_final: 0.8750 (p0) REVERT: B 121 MET cc_start: 0.4719 (mpp) cc_final: 0.4454 (mpp) REVERT: B 232 LYS cc_start: 0.7318 (mmtt) cc_final: 0.6612 (tptt) REVERT: B 645 MET cc_start: 0.6515 (ppp) cc_final: 0.6114 (ppp) REVERT: B 741 ASN cc_start: 0.8924 (m-40) cc_final: 0.8659 (p0) REVERT: C 121 MET cc_start: 0.4533 (mpp) cc_final: 0.4229 (mpp) REVERT: C 232 LYS cc_start: 0.7377 (mmtt) cc_final: 0.6625 (tptt) REVERT: C 616 LEU cc_start: 0.8158 (pp) cc_final: 0.7777 (pp) REVERT: C 741 ASN cc_start: 0.8912 (m-40) cc_final: 0.8638 (p0) REVERT: D 121 MET cc_start: 0.4765 (mpp) cc_final: 0.4467 (mpp) REVERT: D 232 LYS cc_start: 0.7524 (mmtt) cc_final: 0.6782 (tptt) REVERT: D 741 ASN cc_start: 0.8954 (m-40) cc_final: 0.8689 (p0) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3447 time to fit residues: 129.5780 Evaluate side-chains 180 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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: 8.9990 chunk 307 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 322 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 GLN ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 796 HIS ** 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 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 HIS ** 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: 0.6801 moved from start: 0.7031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24572 Z= 0.274 Angle : 1.125 17.810 33448 Z= 0.570 Chirality : 0.059 0.411 3812 Planarity : 0.007 0.116 4340 Dihedral : 8.963 48.524 3456 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 33.73 Ramachandran Plot: Outliers : 0.50 % Allowed : 22.65 % Favored : 76.86 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.49 % Twisted Proline : 4.89 % Twisted General : 1.34 % 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: -3.82 (0.14), residues: 3228 helix: 0.20 (0.17), residues: 1028 sheet: -1.22 (0.39), residues: 164 loop : -4.51 (0.11), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 866 HIS 0.011 0.001 HIS B 129 PHE 0.025 0.002 PHE D 654 TYR 0.031 0.002 TYR A 660 ARG 0.008 0.000 ARG B 787 ********************** 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 234 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.576 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: A 155 CYS cc_start: 0.8041 (m) cc_final: 0.7760 (t) REVERT: A 204 MET cc_start: 0.4041 (tpp) cc_final: 0.3634 (tpt) REVERT: A 232 LYS cc_start: 0.7676 (mmpt) cc_final: 0.7149 (tptt) REVERT: A 307 MET cc_start: 0.4018 (ptm) cc_final: 0.3074 (ttm) REVERT: A 741 ASN cc_start: 0.9127 (m-40) cc_final: 0.8692 (p0) REVERT: A 764 TYR cc_start: 0.7787 (m-10) cc_final: 0.7519 (m-10) REVERT: B 121 MET cc_start: 0.4384 (mpp) cc_final: 0.4100 (mpp) REVERT: B 232 LYS cc_start: 0.7301 (mmtt) cc_final: 0.6595 (tptt) REVERT: B 307 MET cc_start: 0.2866 (ttp) cc_final: 0.2166 (ttp) REVERT: B 618 ILE cc_start: 0.8635 (pt) cc_final: 0.8201 (pt) REVERT: B 722 LEU cc_start: 0.8967 (mt) cc_final: 0.8744 (mt) REVERT: B 741 ASN cc_start: 0.9047 (m-40) cc_final: 0.8616 (p0) REVERT: C 121 MET cc_start: 0.4456 (mpp) cc_final: 0.4131 (mpp) REVERT: C 232 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6631 (tptt) REVERT: C 307 MET cc_start: 0.2852 (ttp) cc_final: 0.2182 (ttp) REVERT: C 741 ASN cc_start: 0.9037 (m-40) cc_final: 0.8632 (p0) REVERT: D 121 MET cc_start: 0.4428 (mpp) cc_final: 0.4097 (mpp) REVERT: D 232 LYS cc_start: 0.7393 (mmtt) cc_final: 0.6635 (tptt) REVERT: D 645 MET cc_start: 0.6278 (ppp) cc_final: 0.5678 (ppp) REVERT: D 741 ASN cc_start: 0.9069 (m-40) cc_final: 0.8651 (p0) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3605 time to fit residues: 135.1523 Evaluate side-chains 180 residues out of total 2728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.915 ------------------------------------------------------------------------------- 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: 3.9990 chunk 273 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 37 optimal weight: 0.0170 chunk 71 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 264 optimal weight: 30.0000 chunk 32 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN C 792 HIS ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 ASN ** D 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 GLN ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.115831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.091968 restraints weight = 158418.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.089725 restraints weight = 156847.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.089732 restraints weight = 139010.963| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.7550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24572 Z= 0.262 Angle : 1.114 17.870 33448 Z= 0.564 Chirality : 0.058 0.415 3812 Planarity : 0.007 0.116 4340 Dihedral : 8.667 46.245 3456 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 31.38 Ramachandran Plot: Outliers : 0.50 % Allowed : 22.03 % Favored : 77.48 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 4.55 % Twisted Proline : 4.35 % Twisted General : 1.08 % 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: -3.75 (0.14), residues: 3228 helix: 0.30 (0.17), residues: 1024 sheet: -0.79 (0.42), residues: 156 loop : -4.50 (0.11), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 866 HIS 0.011 0.001 HIS C 129 PHE 0.032 0.002 PHE A 944 TYR 0.027 0.002 TYR A 660 ARG 0.006 0.000 ARG B 787 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4215.63 seconds wall clock time: 77 minutes 51.56 seconds (4671.56 seconds total)