Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 09:19:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tji_8414/04_2023/5tji_8414_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tji_8414/04_2023/5tji_8414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tji_8414/04_2023/5tji_8414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tji_8414/04_2023/5tji_8414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tji_8414/04_2023/5tji_8414_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tji_8414/04_2023/5tji_8414_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 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 164 5.16 5 C 18048 2.51 5 N 4560 2.21 5 O 4948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 100": "NH1" <-> "NH2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "C ARG 503": "NH1" <-> "NH2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D ARG 503": "NH1" <-> "NH2" Residue "D PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 614": "NH1" <-> "NH2" Residue "D PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 27720 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 883, 6930 Unusual residues: {'PGW': 1} Classifications: {'peptide': 882, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 33, 'TRANS': 848, None: 1} Not linked: pdbres="LYS A1065 " pdbres="PGW A1101 " Chain breaks: 6 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PGW:plan-1': 1, 'PGW:plan-2': 1, 'PGW:plan-3': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 6930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 883, 6930 Unusual residues: {'PGW': 1} Classifications: {'peptide': 882, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 33, 'TRANS': 848, None: 1} Not linked: pdbres="LYS B1065 " pdbres="PGW B1101 " Chain breaks: 6 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PGW:plan-1': 1, 'PGW:plan-2': 1, 'PGW:plan-3': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 6930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 883, 6930 Unusual residues: {'PGW': 1} Classifications: {'peptide': 882, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 33, 'TRANS': 848, None: 1} Not linked: pdbres="LYS C1065 " pdbres="PGW C1101 " Chain breaks: 6 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PGW:plan-1': 1, 'PGW:plan-2': 1, 'PGW:plan-3': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 6930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 883, 6930 Unusual residues: {'PGW': 1} Classifications: {'peptide': 882, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 33, 'TRANS': 848, None: 1} Not linked: pdbres="LYS D1065 " pdbres="PGW D1101 " Chain breaks: 6 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PGW:plan-1': 1, 'PGW:plan-2': 1, 'PGW:plan-3': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Time building chain proxies: 14.16, per 1000 atoms: 0.51 Number of scatterers: 27720 At special positions: 0 Unit cell: (152.55, 152.55, 125.55, 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 164 16.00 O 4948 8.00 N 4560 7.00 C 18048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.92 Conformation dependent library (CDL) restraints added in 4.2 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 16 sheets defined 48.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 18 through 43 removed outlier: 3.799A pdb=" N SER A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 97 through 123 removed outlier: 3.876A pdb=" N ILE A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 removed outlier: 3.683A pdb=" N PHE A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.540A pdb=" N PHE A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.574A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.784A pdb=" N SER A 205 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix removed outlier: 3.645A pdb=" N LEU A 210 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 211 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 212 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 248 removed outlier: 3.710A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 274 removed outlier: 4.154A pdb=" N TYR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 316 removed outlier: 3.711A pdb=" N GLY A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.605A pdb=" N ILE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.907A pdb=" N ASN A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 removed outlier: 3.794A pdb=" N GLY A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 4.033A pdb=" N VAL A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 453 through 459 removed outlier: 3.511A pdb=" N ALA A 456 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.612A pdb=" N ILE A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.846A pdb=" N LEU A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.661A pdb=" N LYS A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 600' Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 722 through 725 No H-bonds generated for 'chain 'A' and resid 722 through 725' Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 756 through 764 removed outlier: 4.720A pdb=" N MET A 761 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 782 through 792 removed outlier: 4.317A pdb=" N ARG A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 788 " --> pdb=" O TYR A 784 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 840 through 851 Processing helix chain 'A' and resid 896 through 900 Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 917 through 921 Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.764A pdb=" N MET A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 951 Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.619A pdb=" N GLU A 965 " --> pdb=" O GLN A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 4.314A pdb=" N ASN A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG A 982 " --> pdb=" O VAL A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 removed outlier: 3.955A pdb=" N GLN A 999 " --> pdb=" O PRO A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1016 removed outlier: 3.635A pdb=" N HIS A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 43 removed outlier: 3.799A pdb=" N SER B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 31 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 97 through 123 removed outlier: 3.876A pdb=" N ILE B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 removed outlier: 3.683A pdb=" N PHE B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 No H-bonds generated for 'chain 'B' and resid 164 through 167' Processing helix chain 'B' and resid 170 through 188 removed outlier: 3.540A pdb=" N PHE B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Proline residue: B 180 - end of helix removed outlier: 3.574A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.784A pdb=" N SER B 205 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Proline residue: B 207 - end of helix removed outlier: 3.645A pdb=" N LEU B 210 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR B 211 " --> pdb=" O ASP B 208 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 212 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 248 removed outlier: 3.710A pdb=" N VAL B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 274 removed outlier: 4.154A pdb=" N TYR B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 316 removed outlier: 3.711A pdb=" N GLY B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Proline residue: B 309 - end of helix removed outlier: 3.605A pdb=" N ILE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 removed outlier: 3.907A pdb=" N ASN B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 382 removed outlier: 3.794A pdb=" N GLY B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 removed outlier: 4.033A pdb=" N VAL B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 439 Processing helix chain 'B' and resid 453 through 459 removed outlier: 3.511A pdb=" N ALA B 456 " --> pdb=" O HIS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.612A pdb=" N ILE B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.846A pdb=" N LEU B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 600 removed outlier: 3.661A pdb=" N LYS B 597 " --> pdb=" O ALA B 593 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 593 through 600' Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 722 through 725 No H-bonds generated for 'chain 'B' and resid 722 through 725' Processing helix chain 'B' and resid 729 through 734 Processing helix chain 'B' and resid 756 through 764 removed outlier: 4.720A pdb=" N MET B 761 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Proline residue: B 762 - end of helix Processing helix chain 'B' and resid 782 through 792 removed outlier: 4.317A pdb=" N ARG B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 788 " --> pdb=" O TYR B 784 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 814 Processing helix chain 'B' and resid 840 through 851 Processing helix chain 'B' and resid 896 through 900 Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 917 through 921 Processing helix chain 'B' and resid 929 through 939 removed outlier: 3.764A pdb=" N MET B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 951 Processing helix chain 'B' and resid 957 through 965 removed outlier: 3.619A pdb=" N GLU B 965 " --> pdb=" O GLN B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 4.314A pdb=" N ASN B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG B 982 " --> pdb=" O VAL B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1001 removed outlier: 3.955A pdb=" N GLN B 999 " --> pdb=" O PRO B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1016 removed outlier: 3.635A pdb=" N HIS B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 43 removed outlier: 3.799A pdb=" N SER C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 31 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 41 " --> pdb=" O TYR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 97 through 123 removed outlier: 3.876A pdb=" N ILE C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 119 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 159 removed outlier: 3.683A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 167 No H-bonds generated for 'chain 'C' and resid 164 through 167' Processing helix chain 'C' and resid 170 through 188 removed outlier: 3.540A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Proline residue: C 180 - end of helix removed outlier: 3.574A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.784A pdb=" N SER C 205 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Proline residue: C 207 - end of helix removed outlier: 3.645A pdb=" N LEU C 210 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR C 211 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 212 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 248 removed outlier: 3.710A pdb=" N VAL C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN C 247 " --> pdb=" O HIS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 274 removed outlier: 4.154A pdb=" N TYR C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 316 removed outlier: 3.711A pdb=" N GLY C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Proline residue: C 309 - end of helix removed outlier: 3.605A pdb=" N ILE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 removed outlier: 3.907A pdb=" N ASN C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 382 removed outlier: 3.794A pdb=" N GLY C 378 " --> pdb=" O LEU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 removed outlier: 4.033A pdb=" N VAL C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 439 Processing helix chain 'C' and resid 453 through 459 removed outlier: 3.511A pdb=" N ALA C 456 " --> pdb=" O HIS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 475 through 488 removed outlier: 3.612A pdb=" N ILE C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 540 through 549 removed outlier: 3.846A pdb=" N LEU C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 600 removed outlier: 3.661A pdb=" N LYS C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 593 through 600' Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 722 through 725 No H-bonds generated for 'chain 'C' and resid 722 through 725' Processing helix chain 'C' and resid 729 through 734 Processing helix chain 'C' and resid 756 through 764 removed outlier: 4.720A pdb=" N MET C 761 " --> pdb=" O ASN C 758 " (cutoff:3.500A) Proline residue: C 762 - end of helix Processing helix chain 'C' and resid 782 through 792 removed outlier: 4.317A pdb=" N ARG C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 788 " --> pdb=" O TYR C 784 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 814 Processing helix chain 'C' and resid 840 through 851 Processing helix chain 'C' and resid 896 through 900 Processing helix chain 'C' and resid 913 through 915 No H-bonds generated for 'chain 'C' and resid 913 through 915' Processing helix chain 'C' and resid 917 through 921 Processing helix chain 'C' and resid 929 through 939 removed outlier: 3.764A pdb=" N MET C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 936 " --> pdb=" O SER C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 951 Processing helix chain 'C' and resid 957 through 965 removed outlier: 3.619A pdb=" N GLU C 965 " --> pdb=" O GLN C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 4.314A pdb=" N ASN C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1001 removed outlier: 3.955A pdb=" N GLN C 999 " --> pdb=" O PRO C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1016 removed outlier: 3.635A pdb=" N HIS C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 43 removed outlier: 3.799A pdb=" N SER D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 31 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 32 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 97 through 123 removed outlier: 3.876A pdb=" N ILE D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 159 removed outlier: 3.683A pdb=" N PHE D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 No H-bonds generated for 'chain 'D' and resid 164 through 167' Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.540A pdb=" N PHE D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 3.574A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 213 removed outlier: 3.784A pdb=" N SER D 205 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Proline residue: D 207 - end of helix removed outlier: 3.645A pdb=" N LEU D 210 " --> pdb=" O PRO D 207 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR D 211 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR D 212 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 248 removed outlier: 3.710A pdb=" N VAL D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 247 " --> pdb=" O HIS D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 removed outlier: 4.154A pdb=" N TYR D 268 " --> pdb=" O TRP D 264 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 316 removed outlier: 3.711A pdb=" N GLY D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 307 " --> pdb=" O LEU D 303 " (cutoff:3.500A) Proline residue: D 309 - end of helix removed outlier: 3.605A pdb=" N ILE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.907A pdb=" N ASN D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 382 removed outlier: 3.794A pdb=" N GLY D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 removed outlier: 4.033A pdb=" N VAL D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 439 Processing helix chain 'D' and resid 453 through 459 removed outlier: 3.511A pdb=" N ALA D 456 " --> pdb=" O HIS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 475 through 488 removed outlier: 3.612A pdb=" N ILE D 483 " --> pdb=" O LYS D 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 540 through 549 removed outlier: 3.846A pdb=" N LEU D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 600 removed outlier: 3.661A pdb=" N LYS D 597 " --> pdb=" O ALA D 593 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 593 through 600' Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 722 through 725 No H-bonds generated for 'chain 'D' and resid 722 through 725' Processing helix chain 'D' and resid 729 through 734 Processing helix chain 'D' and resid 756 through 764 removed outlier: 4.720A pdb=" N MET D 761 " --> pdb=" O ASN D 758 " (cutoff:3.500A) Proline residue: D 762 - end of helix Processing helix chain 'D' and resid 782 through 792 removed outlier: 4.317A pdb=" N ARG D 787 " --> pdb=" O ASP D 783 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 788 " --> pdb=" O TYR D 784 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 814 Processing helix chain 'D' and resid 840 through 851 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 913 through 915 No H-bonds generated for 'chain 'D' and resid 913 through 915' Processing helix chain 'D' and resid 917 through 921 Processing helix chain 'D' and resid 929 through 939 removed outlier: 3.764A pdb=" N MET D 934 " --> pdb=" O LEU D 930 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 936 " --> pdb=" O SER D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 951 Processing helix chain 'D' and resid 957 through 965 removed outlier: 3.619A pdb=" N GLU D 965 " --> pdb=" O GLN D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 removed outlier: 4.314A pdb=" N ASN D 981 " --> pdb=" O ALA D 977 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG D 982 " --> pdb=" O VAL D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1001 removed outlier: 3.955A pdb=" N GLN D 999 " --> pdb=" O PRO D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1016 removed outlier: 3.635A pdb=" N HIS D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 471 through 474 removed outlier: 4.056A pdb=" N ALA A 410 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU A 363 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL A 336 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 365 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N GLY A 338 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU A 367 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS A 368 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 525 through 530 removed outlier: 4.867A pdb=" N GLN A 585 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 557 " --> pdb=" O PHE A 587 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 589 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU A 555 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 571 " --> pdb=" O ILE A 558 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.921A pdb=" N VAL A 741 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 779 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 743 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET A 821 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS A 744 " --> pdb=" O MET A 821 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 823 " --> pdb=" O CYS A 744 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE A 746 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 825 " --> pdb=" O PHE A 746 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER A 826 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 986 through 991 removed outlier: 3.519A pdb=" N ARG A 986 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 471 through 474 removed outlier: 4.056A pdb=" N ALA B 410 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU B 363 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 336 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 365 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N GLY B 338 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU B 367 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 368 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 525 through 530 removed outlier: 4.867A pdb=" N GLN B 585 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA B 557 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 589 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU B 555 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 571 " --> pdb=" O ILE B 558 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 776 through 779 removed outlier: 6.921A pdb=" N VAL B 741 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 779 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 743 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET B 821 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS B 744 " --> pdb=" O MET B 821 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 823 " --> pdb=" O CYS B 744 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE B 746 " --> pdb=" O VAL B 823 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 825 " --> pdb=" O PHE B 746 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER B 826 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 986 through 991 removed outlier: 3.519A pdb=" N ARG B 986 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 471 through 474 removed outlier: 4.056A pdb=" N ALA C 410 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU C 363 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL C 336 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 365 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N GLY C 338 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU C 367 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS C 368 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 525 through 530 removed outlier: 4.867A pdb=" N GLN C 585 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 557 " --> pdb=" O PHE C 587 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE C 589 " --> pdb=" O LEU C 555 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU C 555 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 571 " --> pdb=" O ILE C 558 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 776 through 779 removed outlier: 6.921A pdb=" N VAL C 741 " --> pdb=" O ILE C 777 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL C 779 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 743 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET C 821 " --> pdb=" O VAL C 742 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS C 744 " --> pdb=" O MET C 821 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 823 " --> pdb=" O CYS C 744 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE C 746 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C 825 " --> pdb=" O PHE C 746 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER C 826 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 986 through 991 removed outlier: 3.519A pdb=" N ARG C 986 " --> pdb=" O THR C1063 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 471 through 474 removed outlier: 4.056A pdb=" N ALA D 410 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU D 363 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL D 336 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL D 365 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N GLY D 338 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU D 367 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS D 368 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 525 through 530 removed outlier: 4.867A pdb=" N GLN D 585 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 557 " --> pdb=" O PHE D 587 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE D 589 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU D 555 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 571 " --> pdb=" O ILE D 558 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 776 through 779 removed outlier: 6.921A pdb=" N VAL D 741 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL D 779 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 743 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET D 821 " --> pdb=" O VAL D 742 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS D 744 " --> pdb=" O MET D 821 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 823 " --> pdb=" O CYS D 744 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE D 746 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL D 825 " --> pdb=" O PHE D 746 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER D 826 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 986 through 991 removed outlier: 3.519A pdb=" N ARG D 986 " --> pdb=" O THR D1063 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2748 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: 9.81 Time building geometry restraints manager: 10.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8624 1.34 - 1.46: 3808 1.46 - 1.58: 15700 1.58 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 28380 Sorted by residual: bond pdb=" CA ILE B 308 " pdb=" CB ILE B 308 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.35e+01 bond pdb=" CA ILE D 308 " pdb=" CB ILE D 308 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.35e+01 bond pdb=" CA ILE C 308 " pdb=" CB ILE C 308 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.35e+01 bond pdb=" CA ILE A 308 " pdb=" CB ILE A 308 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.35e+01 bond pdb=" CA PRO D 180 " pdb=" C PRO D 180 " ideal model delta sigma weight residual 1.517 1.543 -0.026 9.30e-03 1.16e+04 7.87e+00 ... (remaining 28375 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.74: 736 106.74 - 113.55: 14932 113.55 - 120.35: 11252 120.35 - 127.16: 11356 127.16 - 133.96: 292 Bond angle restraints: 38568 Sorted by residual: angle pdb=" N VAL D 215 " pdb=" CA VAL D 215 " pdb=" C VAL D 215 " ideal model delta sigma weight residual 111.45 106.11 5.34 9.30e-01 1.16e+00 3.30e+01 angle pdb=" N VAL A 215 " pdb=" CA VAL A 215 " pdb=" C VAL A 215 " ideal model delta sigma weight residual 111.45 106.11 5.34 9.30e-01 1.16e+00 3.30e+01 angle pdb=" N VAL C 215 " pdb=" CA VAL C 215 " pdb=" C VAL C 215 " ideal model delta sigma weight residual 111.45 106.11 5.34 9.30e-01 1.16e+00 3.30e+01 angle pdb=" N VAL B 215 " pdb=" CA VAL B 215 " pdb=" C VAL B 215 " ideal model delta sigma weight residual 111.45 106.11 5.34 9.30e-01 1.16e+00 3.30e+01 angle pdb=" N PRO A 180 " pdb=" CA PRO A 180 " pdb=" C PRO A 180 " ideal model delta sigma weight residual 110.70 116.81 -6.11 1.22e+00 6.72e-01 2.51e+01 ... (remaining 38563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.92: 15172 14.92 - 29.84: 1092 29.84 - 44.76: 268 44.76 - 59.68: 92 59.68 - 74.59: 4 Dihedral angle restraints: 16628 sinusoidal: 6336 harmonic: 10292 Sorted by residual: dihedral pdb=" CA ARG B1026 " pdb=" C ARG B1026 " pdb=" N PHE B1027 " pdb=" CA PHE B1027 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ARG D1026 " pdb=" C ARG D1026 " pdb=" N PHE D1027 " pdb=" CA PHE D1027 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ARG A1026 " pdb=" C ARG A1026 " pdb=" N PHE A1027 " pdb=" CA PHE A1027 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 16625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2716 0.043 - 0.087: 1128 0.087 - 0.130: 380 0.130 - 0.173: 164 0.173 - 0.217: 28 Chirality restraints: 4416 Sorted by residual: chirality pdb=" CA ILE C1044 " pdb=" N ILE C1044 " pdb=" C ILE C1044 " pdb=" CB ILE C1044 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A1044 " pdb=" N ILE A1044 " pdb=" C ILE A1044 " pdb=" CB ILE A1044 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B1044 " pdb=" N ILE B1044 " pdb=" C ILE B1044 " pdb=" CB ILE B1044 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4413 not shown) Planarity restraints: 4856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 308 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO D 309 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 309 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 309 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 308 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 309 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 308 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO C 309 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 309 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 309 " 0.022 5.00e-02 4.00e+02 ... (remaining 4853 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 11460 2.97 - 3.45: 27324 3.45 - 3.93: 42728 3.93 - 4.42: 47758 4.42 - 4.90: 81822 Nonbonded interactions: 211092 Sorted by model distance: nonbonded pdb=" O PRO B 490 " pdb=" OH TYR B1060 " model vdw 2.483 2.440 nonbonded pdb=" O PRO A 490 " pdb=" OH TYR A1060 " model vdw 2.483 2.440 nonbonded pdb=" O PRO D 490 " pdb=" OH TYR D1060 " model vdw 2.483 2.440 nonbonded pdb=" O PRO C 490 " pdb=" OH TYR C1060 " model vdw 2.483 2.440 nonbonded pdb=" O VAL D 929 " pdb=" OG SER D 932 " model vdw 2.486 2.440 ... (remaining 211087 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: 1.010 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: 6.270 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 65.640 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.140 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.037 28380 Z= 0.433 Angle : 0.985 6.108 38568 Z= 0.683 Chirality : 0.058 0.217 4416 Planarity : 0.003 0.039 4856 Dihedral : 11.752 74.594 9972 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.99 % Favored : 93.78 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.12), residues: 3472 helix: -1.73 (0.10), residues: 1572 sheet: -3.02 (0.20), residues: 456 loop : -1.88 (0.15), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 120 average time/residue: 0.4399 time to fit residues: 84.3404 Evaluate side-chains 96 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 3.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 30.0000 chunk 266 optimal weight: 40.0000 chunk 148 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 179 optimal weight: 30.0000 chunk 142 optimal weight: 20.0000 chunk 275 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 319 optimal weight: 0.0970 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 HIS A 454 ASN A 894 ASN A 989 GLN B 453 HIS B 454 ASN B 894 ASN B 989 GLN C 453 HIS C 454 ASN C 894 ASN C 989 GLN D 453 HIS D 454 ASN D 894 ASN D 989 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 28380 Z= 0.151 Angle : 0.508 7.299 38568 Z= 0.258 Chirality : 0.038 0.135 4416 Planarity : 0.004 0.041 4856 Dihedral : 4.220 16.663 3812 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3472 helix: 0.01 (0.12), residues: 1736 sheet: -2.22 (0.22), residues: 428 loop : -1.42 (0.16), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 100 average time/residue: 0.4065 time to fit residues: 67.9159 Evaluate side-chains 96 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 3.295 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2758 time to fit residues: 6.5737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 266 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 320 optimal weight: 3.9990 chunk 345 optimal weight: 40.0000 chunk 285 optimal weight: 6.9990 chunk 317 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 485 GLN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN B 485 GLN ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 HIS ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN C 485 GLN ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 HIS ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 GLN ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 28380 Z= 0.205 Angle : 0.532 8.345 38568 Z= 0.268 Chirality : 0.037 0.138 4416 Planarity : 0.003 0.030 4856 Dihedral : 3.895 13.963 3812 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3472 helix: 0.93 (0.13), residues: 1764 sheet: -1.71 (0.22), residues: 444 loop : -1.06 (0.17), residues: 1264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 3.581 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 outliers start: 16 outliers final: 0 residues processed: 104 average time/residue: 0.4165 time to fit residues: 71.7903 Evaluate side-chains 92 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.9980 chunk 240 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 35 optimal weight: 50.0000 chunk 152 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 340 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 28380 Z= 0.217 Angle : 0.530 7.574 38568 Z= 0.265 Chirality : 0.036 0.157 4416 Planarity : 0.003 0.026 4856 Dihedral : 3.903 15.452 3812 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3472 helix: 1.14 (0.13), residues: 1768 sheet: -1.30 (0.21), residues: 484 loop : -0.84 (0.18), residues: 1220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 3.698 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 outliers start: 8 outliers final: 0 residues processed: 100 average time/residue: 0.4244 time to fit residues: 71.5948 Evaluate side-chains 92 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 253 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 235 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 173 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28380 Z= 0.186 Angle : 0.515 7.850 38568 Z= 0.259 Chirality : 0.036 0.159 4416 Planarity : 0.003 0.026 4856 Dihedral : 3.860 18.025 3812 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3472 helix: 1.13 (0.13), residues: 1800 sheet: -0.65 (0.24), residues: 400 loop : -0.64 (0.18), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.421 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 outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4260 time to fit residues: 65.2980 Evaluate side-chains 92 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 20.0000 chunk 306 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 chunk 282 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 ASN ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 ASN ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 28380 Z= 0.161 Angle : 0.493 9.784 38568 Z= 0.248 Chirality : 0.036 0.173 4416 Planarity : 0.003 0.027 4856 Dihedral : 3.708 18.901 3812 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3472 helix: 1.32 (0.13), residues: 1804 sheet: -0.49 (0.24), residues: 440 loop : -0.51 (0.19), residues: 1228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 3.468 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 outliers start: 12 outliers final: 0 residues processed: 104 average time/residue: 0.4086 time to fit residues: 71.1053 Evaluate side-chains 92 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 212 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 28380 Z= 0.129 Angle : 0.503 9.569 38568 Z= 0.251 Chirality : 0.037 0.204 4416 Planarity : 0.003 0.028 4856 Dihedral : 3.626 19.728 3812 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3472 helix: 1.33 (0.13), residues: 1800 sheet: -0.24 (0.26), residues: 400 loop : -0.44 (0.18), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 0.4384 time to fit residues: 70.3154 Evaluate side-chains 100 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2969 time to fit residues: 8.8743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 202 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 231 optimal weight: 40.0000 chunk 167 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 266 optimal weight: 50.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 28380 Z= 0.179 Angle : 0.536 9.998 38568 Z= 0.269 Chirality : 0.036 0.190 4416 Planarity : 0.003 0.028 4856 Dihedral : 3.657 19.785 3812 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3472 helix: 1.39 (0.13), residues: 1800 sheet: -0.33 (0.24), residues: 440 loop : -0.41 (0.19), residues: 1232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 0.4286 time to fit residues: 68.2116 Evaluate side-chains 100 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 3.211 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2839 time to fit residues: 8.3585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 7.9990 chunk 325 optimal weight: 20.0000 chunk 296 optimal weight: 9.9990 chunk 316 optimal weight: 30.0000 chunk 324 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 285 optimal weight: 8.9990 chunk 299 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1016 HIS B1016 HIS C1016 HIS D1016 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 28380 Z= 0.235 Angle : 0.608 15.411 38568 Z= 0.303 Chirality : 0.037 0.176 4416 Planarity : 0.003 0.028 4856 Dihedral : 3.866 20.070 3812 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3472 helix: 1.41 (0.13), residues: 1768 sheet: -0.45 (0.24), residues: 440 loop : -0.33 (0.19), residues: 1264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 3.402 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 outliers start: 4 outliers final: 4 residues processed: 92 average time/residue: 0.4368 time to fit residues: 66.5792 Evaluate side-chains 96 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 3.405 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3021 time to fit residues: 6.7338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 334 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 chunk 350 optimal weight: 2.9990 chunk 322 optimal weight: 8.9990 chunk 279 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 28380 Z= 0.134 Angle : 0.543 12.926 38568 Z= 0.274 Chirality : 0.038 0.201 4416 Planarity : 0.003 0.030 4856 Dihedral : 3.769 20.349 3812 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3472 helix: 1.33 (0.13), residues: 1768 sheet: -0.38 (0.24), residues: 440 loop : -0.44 (0.19), residues: 1264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.398 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 outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4332 time to fit residues: 66.1077 Evaluate side-chains 92 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 297 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 287 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.029876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.023139 restraints weight = 454464.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.023273 restraints weight = 417972.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.023273 restraints weight = 343203.399| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 28380 Z= 0.172 Angle : 0.552 9.813 38568 Z= 0.281 Chirality : 0.037 0.168 4416 Planarity : 0.003 0.030 4856 Dihedral : 3.729 20.267 3812 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3472 helix: 1.34 (0.13), residues: 1792 sheet: -0.32 (0.24), residues: 440 loop : -0.41 (0.19), residues: 1240 =============================================================================== Job complete usr+sys time: 3474.39 seconds wall clock time: 66 minutes 9.23 seconds (3969.23 seconds total)