Starting phenix.real_space_refine (version: dev) on Mon Feb 20 04:24:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txz_26162/02_2023/7txz_26162.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txz_26162/02_2023/7txz_26162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txz_26162/02_2023/7txz_26162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txz_26162/02_2023/7txz_26162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txz_26162/02_2023/7txz_26162.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txz_26162/02_2023/7txz_26162.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 554": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "E GLU 1": "OE1" <-> "OE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11303 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3513 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3579 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 438} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 882 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 835 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 874 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 805 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 212 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 29} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 205 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 29} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.60, per 1000 atoms: 0.58 Number of scatterers: 11303 At special positions: 0 Unit cell: (101.85, 134.4, 143.85, 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 74 16.00 O 2077 8.00 N 1914 7.00 C 7238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS D 162 " distance=2.06 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS D 158 " distance=2.04 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.02 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.12 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.05 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS D 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 158 " - pdb=" SG CYS C 162 " distance=2.07 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS C 158 " distance=2.04 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 601 " distance=2.02 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.02 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.11 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.06 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.02 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 3 " NAG-ASN " NAG A 701 " - " ASN A 378 " " NAG G 1 " - " ASN A 306 " " NAG I 1 " - " ASN A 417 " " NAG J 1 " - " ASN A 529 " " NAG K 1 " - " ASN A 481 " " NAG M 1 " - " ASN A 159 " " NAG N 1 " - " ASN B 306 " " NAG O 1 " - " ASN B 378 " " NAG P 1 " - " ASN B 417 " " NAG Q 1 " - " ASN B 481 " " NAG R 1 " - " ASN B 529 " " NAG S 1 " - " ASN B 159 " " NAG T 1 " - " ASN D 159 " " NAG U 1 " - " ASN C 159 " Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 30 sheets defined 9.9% alpha, 43.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 76 through 78 No H-bonds generated for 'chain 'H' and resid 76 through 78' Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'D' and resid 133 through 146 Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.571A pdb=" N ASN C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 6.076A pdb=" N LEU A 153 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 153 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.826A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 225 removed outlier: 6.405A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A 224 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE A 229 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL A 252 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR A 231 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 250 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS A 233 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG A 248 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU A 235 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 256 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU A 265 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 287 removed outlier: 5.575A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 341 removed outlier: 3.536A pdb=" N LYS A 347 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 447 removed outlier: 4.194A pdb=" N LYS A 465 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 468 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.404A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLN A 550 " --> pdb=" O PRO A 535 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A 537 " --> pdb=" O ARG A 548 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG A 548 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 539 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 180 removed outlier: 4.828A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 592 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 215 through 225 removed outlier: 6.420A pdb=" N SER B 232 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU B 222 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 230 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET B 224 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 247 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 237 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER B 245 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU B 265 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 279 through 287 removed outlier: 5.495A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 340 through 341 removed outlier: 3.546A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AB6, first strand: chain 'B' and resid 442 through 447 removed outlier: 4.220A pdb=" N LYS B 465 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.558A pdb=" N ILE B 520 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN B 550 " --> pdb=" O PRO B 535 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE B 537 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.448A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP E 33 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.448A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS E 98 " --> pdb=" O TRP E 109 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP E 109 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG E 100 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.202A pdb=" N LEU F 11 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS F 111 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL F 13 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP F 39 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.202A pdb=" N LEU F 11 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS F 111 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL F 13 " --> pdb=" O LYS F 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.205A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.205A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N CYS H 98 " --> pdb=" O TRP H 109 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TRP H 109 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG H 100 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.022A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL L 13 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.022A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL L 13 " --> pdb=" O LYS L 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 30 through 31 468 hydrogen bonds defined for protein. 1155 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: 4.30 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2864 1.33 - 1.46: 3177 1.46 - 1.59: 5433 1.59 - 1.72: 5 1.72 - 1.85: 98 Bond restraints: 11577 Sorted by residual: bond pdb=" C5 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.10e-02 8.26e+03 1.85e+01 bond pdb=" C3 NAG I 1 " pdb=" C4 NAG I 1 " ideal model delta sigma weight residual 1.523 1.565 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" C5 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.10e-02 8.26e+03 1.73e+01 bond pdb=" C5 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.10e-02 8.26e+03 1.71e+01 bond pdb=" C5 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.10e-02 8.26e+03 1.69e+01 ... (remaining 11572 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.67: 283 104.67 - 112.00: 5443 112.00 - 119.32: 3880 119.32 - 126.65: 6064 126.65 - 133.97: 123 Bond angle restraints: 15793 Sorted by residual: angle pdb=" C CYS A 493 " pdb=" N PRO A 494 " pdb=" CA PRO A 494 " ideal model delta sigma weight residual 120.21 127.93 -7.72 9.60e-01 1.09e+00 6.47e+01 angle pdb=" C ASP B 302 " pdb=" N PRO B 303 " pdb=" CA PRO B 303 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.39e+01 angle pdb=" C LYS A 391 " pdb=" N PRO A 392 " pdb=" CA PRO A 392 " ideal model delta sigma weight residual 119.56 127.37 -7.81 1.02e+00 9.61e-01 5.87e+01 angle pdb=" C THR B 272 " pdb=" N PRO B 273 " pdb=" CA PRO B 273 " ideal model delta sigma weight residual 119.66 125.13 -5.47 7.20e-01 1.93e+00 5.77e+01 angle pdb=" C LYS A 322 " pdb=" N PRO A 323 " pdb=" CA PRO A 323 " ideal model delta sigma weight residual 119.78 127.29 -7.51 1.03e+00 9.43e-01 5.32e+01 ... (remaining 15788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6623 17.95 - 35.89: 172 35.89 - 53.84: 51 53.84 - 71.79: 23 71.79 - 89.73: 7 Dihedral angle restraints: 6876 sinusoidal: 2634 harmonic: 4242 Sorted by residual: dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS C 146 " pdb=" CB CYS C 146 " ideal model delta sinusoidal sigma weight residual 93.00 -177.27 -89.73 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 395 " pdb=" CB CYS A 395 " ideal model delta sinusoidal sigma weight residual -86.00 -159.74 73.74 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS B 387 " pdb=" SG CYS B 387 " pdb=" SG CYS B 499 " pdb=" CB CYS B 499 " ideal model delta sinusoidal sigma weight residual 93.00 155.17 -62.17 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 6873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1249 0.078 - 0.157: 458 0.157 - 0.235: 87 0.235 - 0.313: 25 0.313 - 0.391: 28 Chirality restraints: 1847 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.11e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.93e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.90e+01 ... (remaining 1844 not shown) Planarity restraints: 2021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 481 " 0.048 2.00e-02 2.50e+03 4.86e-02 2.96e+01 pdb=" CG ASN A 481 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 481 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 481 " -0.074 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 481 " 0.040 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" CG ASN B 481 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 481 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 481 " -0.062 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 159 " -0.030 2.00e-02 2.50e+03 3.05e-02 1.16e+01 pdb=" CG ASN A 159 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 159 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 159 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.037 2.00e-02 2.50e+03 ... (remaining 2018 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4396 2.90 - 3.40: 9695 3.40 - 3.90: 19242 3.90 - 4.40: 21941 4.40 - 4.90: 36750 Nonbonded interactions: 92024 Sorted by model distance: nonbonded pdb=" O ARG A 435 " pdb=" NZ LYS A 465 " model vdw 2.400 2.520 nonbonded pdb=" OD2 ASP A 420 " pdb=" NZ LYS A 425 " model vdw 2.421 2.520 nonbonded pdb=" N THR B 149 " pdb=" O THR B 149 " model vdw 2.476 2.496 nonbonded pdb=" N ASP B 360 " pdb=" OD1 ASP B 360 " model vdw 2.490 2.520 nonbonded pdb=" N ASP B 433 " pdb=" OD1 ASP B 433 " model vdw 2.509 2.520 ... (remaining 92019 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' and ((resid 132 through 144 and (name N or name CA or name C or name \ O or name CB )) or resid 145 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 197 through 203 or (resid 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 through 208 or (res \ id 209 through 210 and (name N or name CA or name C or name O or name CB )) or r \ esid 211 through 238 or (resid 239 and (name N or name CA or name C or name O or \ name CB )) or resid 240 through 263 or (resid 264 and (name N or name CA or nam \ e C or name O or name CB )) or resid 265 through 288 or (resid 289 and (name N o \ r name CA or name C or name O or name CB )) or resid 290 through 312 or (resid 3 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 314 through \ 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) or r \ esid 375 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 410 or (resid 411 and (name N or name CA or nam \ e C or name O or name CB )) or resid 412 through 422 or (resid 423 and (name N o \ r name CA or name C or name O or name CB )) or resid 424 through 439 or (resid 4 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 441 through \ 514 or (resid 515 and (name N or name CA or name C or name O or name CB )) or r \ esid 516 through 553 or (resid 554 through 555 and (name N or name CA or name C \ or name O or name CB )) or resid 556 through 581 or (resid 582 through 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 602)) selection = (chain 'B' and (resid 132 through 160 or (resid 161 and (name N or name CA or na \ me C or name O or name CB )) or resid 162 through 163 or (resid 164 and (name N \ or name CA or name C or name O or name CB )) or resid 165 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throug \ h 173 or (resid 174 through 176 and (name N or name CA or name C or name O or na \ me CB )) or resid 177 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 218 or (resid 219 and (name N or n \ ame CA or name C or name O or name CB )) or resid 220 through 225 or (resid 226 \ and (name N or name CA or name C or name O or name CB )) or resid 227 through 23 \ 4 or (resid 235 and (name N or name CA or name C or name O or name CB )) or resi \ d 236 through 241 or (resid 242 and (name N or name CA or name C or name O or na \ me CB )) or resid 243 through 245 or (resid 246 and (name N or name CA or name C \ or name O or name CB )) or resid 247 through 271 or (resid 272 and (name N or n \ ame CA or name C or name O or name CB )) or resid 273 through 287 or (resid 288 \ through 289 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 0 through 298 or (resid 299 and (name N or name CA or name C or name O or name C \ B )) or resid 300 through 306 or (resid 307 through 308 and (name N or name CA o \ r name C or name O or name CB )) or resid 309 through 325 or (resid 326 and (nam \ e N or name CA or name C or name O or name CB )) or resid 327 through 337 or (re \ sid 338 through 339 and (name N or name CA or name C or name O or name CB )) or \ resid 340 through 345 or (resid 346 and (name N or name CA or name C or name O o \ r name CB )) or resid 347 through 359 or (resid 360 and (name N or name CA or na \ me C or name O or name CB )) or resid 361 through 375 or (resid 376 and (name N \ or name CA or name C or name O or name CB )) or resid 377 through 380 or (resid \ 381 and (name N or name CA or name C or name O or name CB )) or resid 382 throug \ h 383 or (resid 384 through 386 and (name N or name CA or name C or name O or na \ me CB )) or resid 387 through 390 or (resid 391 and (name N or name CA or name C \ or name O or name CB )) or resid 392 or (resid 393 and (name N or name CA or na \ me C or name O or name CB )) or resid 394 through 432 or (resid 433 and (name N \ or name CA or name C or name O or name CB )) or resid 434 through 470 or (resid \ 471 and (name N or name CA or name C or name O or name CB )) or resid 472 throug \ h 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) or \ resid 502 through 504 or (resid 505 and (name N or name CA or name C or name O o \ r name CB )) or resid 506 through 526 or (resid 527 through 528 and (name N or n \ ame CA or name C or name O or name CB )) or resid 529 through 532 or (resid 533 \ and (name N or name CA or name C or name O or name CB )) or resid 534 through 58 \ 2 or resid 585 through 602)) } ncs_group { reference = (chain 'C' and (resid 132 through 152 or (resid 153 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 165)) selection = (chain 'D' and ((resid 132 through 145 and (name N or name CA or name C or name \ O or name CB )) or resid 146 through 156 or (resid 157 and (name N or name CA or \ name C or name O or name CB )) or resid 158 through 165)) } ncs_group { reference = (chain 'E' and (resid 1 through 10 or (resid 11 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 20 or (resid 21 and (nam \ e N or name CA or name C or name O or name CB )) or resid 22 through 24 or (resi \ d 25 and (name N or name CA or name C or name O or name CB )) or resid 26 throug \ h 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or re \ sid 68 through 85 or (resid 86 through 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or \ name C or name O or name CB )) or resid 92 or (resid 93 and (name N or name CA \ or name C or name O or name CB )) or resid 94 through 117)) selection = (chain 'H' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 72 or (resid 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 77 and (name N or name CA or name C or name O or name CB )) or resid 78 thro \ ugh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or \ resid 88 through 117)) } ncs_group { reference = (chain 'F' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 or (resid 5 and (name N or name CA or name C or name O o \ r name CB )) or resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 13 or (resid 14 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 through 19 or (resid 20 and (n \ ame N or name CA or name C or name O or name CB )) or resid 21 or (resid 22 and \ (name N or name CA or name C or name O or name CB )) or resid 23 through 25 or ( \ resid 26 through 28 and (name N or name CA or name C or name O or name CB )) or \ resid 29 through 66 or (resid 67 and (name N or name CA or name C or name O or n \ ame CB )) or resid 68 or (resid 69 and (name N or name CA or name C or name O or \ name CB )) or resid 70 or (resid 71 and (name N or name CA or name C or name O \ or name CB )) or resid 72 or (resid 73 through 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 or (resid 76 and (name N or name CA or na \ me C or name O or name CB )) or resid 77 through 83 or (resid 84 through 85 and \ (name N or name CA or name C or name O or name CB )) or resid 86 through 111)) selection = (chain 'L' and resid 2 through 111) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7238 2.51 5 N 1914 2.21 5 O 2077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.910 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: 0.010 Extract box with map and model: 21.000 Check model and map are aligned: 0.160 Process input model: 32.550 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 0.105 11577 Z= 1.079 Angle : 1.482 8.739 15793 Z= 1.028 Chirality : 0.094 0.391 1847 Planarity : 0.006 0.068 2007 Dihedral : 10.073 86.530 4086 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.22), residues: 1446 helix: 0.62 (0.64), residues: 58 sheet: 0.97 (0.22), residues: 524 loop : 0.23 (0.21), residues: 864 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 1.325 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 239 average time/residue: 0.2789 time to fit residues: 90.9024 Evaluate side-chains 154 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 109 optimal weight: 0.0070 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN B 478 ASN B 557 ASN B 600 GLN F 46 GLN ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN D 139 ASN C 156 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11577 Z= 0.232 Angle : 0.631 13.091 15793 Z= 0.339 Chirality : 0.048 0.282 1847 Planarity : 0.004 0.043 2007 Dihedral : 5.136 21.997 1760 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.87 % Favored : 98.06 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.65 (0.22), residues: 1446 helix: 1.90 (0.71), residues: 60 sheet: 0.79 (0.22), residues: 548 loop : 0.17 (0.22), residues: 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 188 average time/residue: 0.2661 time to fit residues: 70.1244 Evaluate side-chains 153 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.248 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1107 time to fit residues: 3.8197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 36 optimal weight: 0.0170 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 105 optimal weight: 0.1980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 358 GLN A 559 GLN B 187 ASN B 509 ASN B 543 ASN H 84 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 11577 Z= 0.240 Angle : 0.568 11.095 15793 Z= 0.300 Chirality : 0.047 0.296 1847 Planarity : 0.004 0.049 2007 Dihedral : 4.875 27.730 1760 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.54 (0.22), residues: 1446 helix: 2.19 (0.73), residues: 64 sheet: 0.65 (0.22), residues: 551 loop : 0.08 (0.22), residues: 831 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 181 average time/residue: 0.2479 time to fit residues: 64.5231 Evaluate side-chains 166 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1139 time to fit residues: 3.4176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 559 GLN B 174 GLN F 58 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 11577 Z= 0.242 Angle : 0.533 6.812 15793 Z= 0.281 Chirality : 0.047 0.296 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.690 16.865 1760 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.49 % Favored : 97.44 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.46 (0.22), residues: 1446 helix: 2.15 (0.73), residues: 65 sheet: 0.64 (0.22), residues: 553 loop : -0.01 (0.22), residues: 828 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 0.2406 time to fit residues: 58.8766 Evaluate side-chains 155 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1275 time to fit residues: 3.3914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.0370 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 GLN A 559 GLN H 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 11577 Z= 0.240 Angle : 0.539 9.850 15793 Z= 0.282 Chirality : 0.047 0.299 1847 Planarity : 0.004 0.052 2007 Dihedral : 4.686 27.432 1760 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.30 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.41 (0.22), residues: 1446 helix: 2.58 (0.76), residues: 62 sheet: 0.61 (0.22), residues: 549 loop : -0.07 (0.22), residues: 835 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 163 average time/residue: 0.2376 time to fit residues: 56.3338 Evaluate side-chains 148 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1218 time to fit residues: 2.5236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 chunk 64 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11577 Z= 0.174 Angle : 0.509 10.459 15793 Z= 0.264 Chirality : 0.046 0.298 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.555 27.083 1760 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.41 (0.22), residues: 1446 helix: 2.04 (0.74), residues: 68 sheet: 0.68 (0.22), residues: 543 loop : -0.10 (0.22), residues: 835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 163 average time/residue: 0.2370 time to fit residues: 56.1303 Evaluate side-chains 157 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1295 time to fit residues: 2.8769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 11577 Z= 0.227 Angle : 0.541 11.424 15793 Z= 0.280 Chirality : 0.047 0.299 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.619 27.558 1760 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.36 (0.22), residues: 1446 helix: 2.07 (0.73), residues: 67 sheet: 0.67 (0.22), residues: 542 loop : -0.15 (0.22), residues: 837 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 160 average time/residue: 0.2482 time to fit residues: 57.6831 Evaluate side-chains 154 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1164 time to fit residues: 2.4986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 11577 Z= 0.313 Angle : 0.575 11.463 15793 Z= 0.299 Chirality : 0.048 0.310 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.745 28.463 1760 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.24 (0.22), residues: 1446 helix: 2.45 (0.74), residues: 61 sheet: 0.59 (0.22), residues: 543 loop : -0.26 (0.21), residues: 842 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 159 average time/residue: 0.2747 time to fit residues: 62.8077 Evaluate side-chains 143 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1273 time to fit residues: 2.9665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11577 Z= 0.193 Angle : 0.527 9.868 15793 Z= 0.274 Chirality : 0.046 0.312 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.630 27.016 1760 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.25 (0.22), residues: 1446 helix: 2.06 (0.73), residues: 67 sheet: 0.60 (0.23), residues: 543 loop : -0.23 (0.22), residues: 836 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.275 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 151 average time/residue: 0.2488 time to fit residues: 53.7277 Evaluate side-chains 145 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1555 time to fit residues: 1.9047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 11577 Z= 0.210 Angle : 0.527 9.878 15793 Z= 0.273 Chirality : 0.047 0.309 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.593 26.874 1760 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.22), residues: 1446 helix: 2.14 (0.72), residues: 67 sheet: 0.61 (0.23), residues: 543 loop : -0.24 (0.22), residues: 836 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 144 average time/residue: 0.2576 time to fit residues: 53.6381 Evaluate side-chains 140 residues out of total 1303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1003 time to fit residues: 1.9169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 114 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.149274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119039 restraints weight = 14145.237| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.15 r_work: 0.3133 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11577 Z= 0.198 Angle : 0.520 9.475 15793 Z= 0.268 Chirality : 0.046 0.308 1847 Planarity : 0.004 0.051 2007 Dihedral : 4.534 26.357 1760 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.27 (0.22), residues: 1446 helix: 2.22 (0.73), residues: 67 sheet: 0.63 (0.23), residues: 541 loop : -0.25 (0.22), residues: 838 =============================================================================== Job complete usr+sys time: 2815.93 seconds wall clock time: 52 minutes 16.91 seconds (3136.91 seconds total)