Starting phenix.real_space_refine on Mon Feb 19 20:57:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/02_2024/7ffl_31568_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/02_2024/7ffl_31568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/02_2024/7ffl_31568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/02_2024/7ffl_31568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/02_2024/7ffl_31568_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffl_31568/02_2024/7ffl_31568_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.008 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 201 5.16 5 C 16302 2.51 5 N 4410 2.21 5 O 4851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 161": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J ARG 419": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 103": "NH1" <-> "NH2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "Q ARG 281": "NH1" <-> "NH2" Residue "Q ARG 419": "NH1" <-> "NH2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 103": "NH1" <-> "NH2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 281": "NH1" <-> "NH2" Residue "R ARG 407": "NH1" <-> "NH2" Residue "R ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25767 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "E" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "G" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "H" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "I" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "R" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "T" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.17, per 1000 atoms: 0.51 Number of scatterers: 25767 At special positions: 0 Unit cell: (158.4, 199.32, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 201 16.00 O 4851 8.00 N 4410 7.00 C 16302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.04 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 55 " distance=2.00 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 42 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 55 " distance=1.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 64 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 42 " distance=2.03 Simple disulfide: pdb=" SG CYS H 37 " - pdb=" SG CYS H 55 " distance=1.25 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 64 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS I 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 27 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS J 151 " - pdb=" SG CYS J 266 " distance=2.03 Simple disulfide: pdb=" SG CYS J 200 " - pdb=" SG CYS J 226 " distance=2.03 Simple disulfide: pdb=" SG CYS J 202 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=1.56 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 27 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 151 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 226 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 16 " distance=2.03 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: 9.81 Conformation dependent library (CDL) restraints added in 4.6 seconds 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 69 sheets defined 16.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.094A pdb=" N MET A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.858A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.238A pdb=" N ALA A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.542A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 404 through 438 removed outlier: 4.834A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.730A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.662A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 404 through 439 removed outlier: 3.665A pdb=" N LEU C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.902A pdb=" N SER E 59 " --> pdb=" O PHE E 56 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP E 60 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS E 62 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 removed outlier: 4.743A pdb=" N ASP F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.648A pdb=" N ALA F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.566A pdb=" N ARG F 185 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 289 through 293 removed outlier: 3.586A pdb=" N GLU G 292 " --> pdb=" O ARG G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 4.758A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 55 through 62 removed outlier: 4.434A pdb=" N SER H 59 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP H 60 " --> pdb=" O ASP H 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.968A pdb=" N VAL I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 removed outlier: 4.545A pdb=" N LYS I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 351 through 363 removed outlier: 3.785A pdb=" N VAL J 355 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE J 356 " --> pdb=" O PRO J 352 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR J 357 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 398 removed outlier: 3.862A pdb=" N ILE J 368 " --> pdb=" O PRO J 364 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU J 369 " --> pdb=" O MET J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 416 Processing helix chain 'P' and resid 28 through 37 removed outlier: 3.593A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN P 37 " --> pdb=" O MET P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 52 removed outlier: 4.207A pdb=" N LYS P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.532A pdb=" N THR Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'Q' and resid 354 through 363 Processing helix chain 'Q' and resid 363 through 402 removed outlier: 3.774A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU Q 369 " --> pdb=" O MET Q 365 " (cutoff:3.500A) Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 409 through 416 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 8 through 12 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 222 through 224 No H-bonds generated for 'chain 'R' and resid 222 through 224' Processing helix chain 'R' and resid 352 through 363 removed outlier: 3.736A pdb=" N ILE R 356 " --> pdb=" O PRO R 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 398 removed outlier: 3.862A pdb=" N ILE R 368 " --> pdb=" O PRO R 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 369 " --> pdb=" O MET R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 401 No H-bonds generated for 'chain 'R' and resid 399 through 401' Processing helix chain 'R' and resid 410 through 416 Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.873A pdb=" N ALA S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 removed outlier: 3.591A pdb=" N ARG S 185 " --> pdb=" O GLN S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.098A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN T 37 " --> pdb=" O MET T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 52 removed outlier: 3.654A pdb=" N LEU T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS T 52 " --> pdb=" O GLU T 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.734A pdb=" N TYR A 139 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 143 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 8.098A pdb=" N ALA A 206 " --> pdb=" O PRO A 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 214 through 217 current: chain 'A' and resid 239 through 247 removed outlier: 7.859A pdb=" N ALA A 239 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TRP A 258 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 241 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 256 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 243 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 250 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 31 current: chain 'B' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 147 current: chain 'B' and resid 183 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 61 removed outlier: 4.752A pdb=" N LYS B 105 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 103 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 60 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 101 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.307A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.647A pdb=" N CYS B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 147 current: chain 'C' and resid 183 through 185 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 55 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.699A pdb=" N GLY C 91 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.405A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC3, first strand: chain 'C' and resid 364 through 369 Processing sheet with id=AC4, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AC5, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AC7, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.640A pdb=" N VAL F 143 " --> pdb=" O LYS F 146 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU F 132 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 138 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 190 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 190 through 191 current: chain 'F' and resid 205 through 209 removed outlier: 8.538A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 214 through 217 current: chain 'F' and resid 236 through 246 removed outlier: 5.774A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD1, first strand: chain 'G' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 27 through 31 current: chain 'G' and resid 119 through 137 removed outlier: 3.505A pdb=" N THR G 144 " --> pdb=" O LEU G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 141 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AD2, first strand: chain 'G' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 55 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD4, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD5, first strand: chain 'G' and resid 296 through 306 removed outlier: 5.337A pdb=" N ALA G 298 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER G 321 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AD7, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AD8, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD9, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AE1, first strand: chain 'I' and resid 6 through 8 removed outlier: 3.616A pdb=" N PHE I 14 " --> pdb=" O CYS I 7 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AE3, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.587A pdb=" N GLN J 48 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL J 36 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG J 46 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N SER J 50 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP J 69 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR J 65 " --> pdb=" O GLY J 54 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.504A pdb=" N ILE J 110 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 147 through 149 Processing sheet with id=AE6, first strand: chain 'J' and resid 152 through 154 Processing sheet with id=AE7, first strand: chain 'J' and resid 237 through 238 removed outlier: 3.534A pdb=" N VAL J 237 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY J 253 " --> pdb=" O MET J 167 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 179 through 181 Processing sheet with id=AE9, first strand: chain 'J' and resid 196 through 200 removed outlier: 3.983A pdb=" N LEU J 197 " --> pdb=" O TYR J 229 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 275 through 279 Processing sheet with id=AF2, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AF3, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AF4, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.623A pdb=" N GLN Q 48 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR Q 65 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AF6, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AF7, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.785A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 179 through 181 removed outlier: 4.120A pdb=" N VAL Q 186 " --> pdb=" O PHE Q 217 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AG1, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AG2, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AG3, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.795A pdb=" N GLN R 48 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL R 36 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG R 46 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N SER R 50 " --> pdb=" O ASP R 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AG5, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AG6, first strand: chain 'R' and resid 237 through 238 removed outlier: 3.629A pdb=" N GLY R 253 " --> pdb=" O MET R 167 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.879A pdb=" N VAL R 186 " --> pdb=" O PHE R 217 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.562A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AH1, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.655A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AH3, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AH4, first strand: chain 'S' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS S 190 " --> pdb=" O VAL S 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.496A pdb=" N ALA S 206 " --> pdb=" O PRO S 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 213 through 217 current: chain 'S' and resid 239 through 245 removed outlier: 6.156A pdb=" N VAL S 241 " --> pdb=" O VAL S 256 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL S 256 " --> pdb=" O VAL S 241 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.516A pdb=" N PHE T 14 " --> pdb=" O CYS T 7 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1962 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: 8.24 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8253 1.34 - 1.46: 6441 1.46 - 1.59: 11475 1.59 - 1.71: 0 1.71 - 1.84: 264 Bond restraints: 26433 Sorted by residual: bond pdb=" CB VAL G 148 " pdb=" CG2 VAL G 148 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.75e+00 bond pdb=" CB VAL C 148 " pdb=" CG2 VAL C 148 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.56e+00 bond pdb=" CB VAL G 42 " pdb=" CG1 VAL G 42 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.54e+00 bond pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.83e+00 bond pdb=" C ASN G 264 " pdb=" N PRO G 265 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.74e+00 ... (remaining 26428 not shown) Histogram of bond angle deviations from ideal: 98.16 - 108.50: 2251 108.50 - 118.84: 19218 118.84 - 129.18: 14292 129.18 - 139.52: 214 139.52 - 149.86: 1 Bond angle restraints: 35976 Sorted by residual: angle pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" C PRO R 409 " ideal model delta sigma weight residual 112.47 149.86 -37.39 2.06e+00 2.36e-01 3.29e+02 angle pdb=" N PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta sigma weight residual 110.49 132.07 -21.58 1.69e+00 3.50e-01 1.63e+02 angle pdb=" N LYS D 58 " pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 111.39 123.04 -11.65 1.38e+00 5.25e-01 7.12e+01 angle pdb=" N LYS H 58 " pdb=" CA LYS H 58 " pdb=" C LYS H 58 " ideal model delta sigma weight residual 111.54 120.30 -8.76 1.36e+00 5.41e-01 4.15e+01 angle pdb=" N PHE H 56 " pdb=" CA PHE H 56 " pdb=" C PHE H 56 " ideal model delta sigma weight residual 109.96 100.78 9.18 1.50e+00 4.44e-01 3.75e+01 ... (remaining 35971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 14964 14.33 - 28.65: 732 28.65 - 42.98: 189 42.98 - 57.31: 31 57.31 - 71.64: 20 Dihedral angle restraints: 15936 sinusoidal: 6261 harmonic: 9675 Sorted by residual: dihedral pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual 115.10 155.02 -39.92 0 2.50e+00 1.60e-01 2.55e+02 dihedral pdb=" C PRO R 409 " pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual -120.70 -155.07 34.37 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta harmonic sigma weight residual 122.80 157.10 -34.30 0 2.50e+00 1.60e-01 1.88e+02 ... (remaining 15933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 3981 0.403 - 0.806: 4 0.806 - 1.209: 0 1.209 - 1.612: 1 1.612 - 2.014: 1 Chirality restraints: 3987 Sorted by residual: chirality pdb=" CA PRO R 409 " pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CB PRO R 409 " both_signs ideal model delta sigma weight residual False 2.72 0.70 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA PHE R 410 " pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CB PHE R 410 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.63e+01 chirality pdb=" CA LYS D 58 " pdb=" N LYS D 58 " pdb=" C LYS D 58 " pdb=" CB LYS D 58 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 3984 not shown) Planarity restraints: 4647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 265 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 236 " -0.039 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" CG TRP J 236 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J 236 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP J 236 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 236 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J 236 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 236 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 236 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 236 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J 236 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 264 " 0.057 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO B 265 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " 0.049 5.00e-02 4.00e+02 ... (remaining 4644 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 376 2.65 - 3.22: 21300 3.22 - 3.78: 37781 3.78 - 4.34: 51412 4.34 - 4.90: 86899 Nonbonded interactions: 197768 Sorted by model distance: nonbonded pdb=" OD1 ASP D 57 " pdb=" OG SER J 177 " model vdw 2.092 2.440 nonbonded pdb=" O HIS G 441 " pdb=" OXT ASN G 442 " model vdw 2.236 3.040 nonbonded pdb=" O ALA C 401 " pdb=" OH TYR R 359 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLU B 120 " pdb=" OH TYR B 122 " model vdw 2.269 2.440 nonbonded pdb=" O ALA B 401 " pdb=" OH TYR Q 359 " model vdw 2.272 2.440 ... (remaining 197763 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 'F' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'R' } 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 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: 0.980 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: 0.030 Extract box with map and model: 5.210 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 64.140 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.200 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: 75.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 0.103 26433 Z= 0.499 Angle : 0.964 37.389 35976 Z= 0.532 Chirality : 0.071 2.014 3987 Planarity : 0.008 0.102 4647 Dihedral : 9.546 71.636 9591 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.65 % Favored : 93.19 % Rotamer: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.20 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % 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: -3.39 (0.12), residues: 3306 helix: -2.35 (0.18), residues: 435 sheet: -1.84 (0.16), residues: 909 loop : -2.50 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP J 236 HIS 0.010 0.002 HIS J 288 PHE 0.032 0.004 PHE Q 328 TYR 0.039 0.003 TYR C 308 ARG 0.015 0.001 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 649 time to evaluate : 2.944 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: A 180 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7298 (t) REVERT: A 200 TYR cc_start: 0.6210 (m-80) cc_final: 0.5619 (m-80) REVERT: A 267 TYR cc_start: 0.6714 (t80) cc_final: 0.6229 (t80) REVERT: B 55 MET cc_start: 0.8105 (mtm) cc_final: 0.7902 (mtm) REVERT: C 115 LEU cc_start: 0.8423 (tm) cc_final: 0.8192 (tp) REVERT: C 354 ILE cc_start: 0.8152 (pt) cc_final: 0.7800 (mt) REVERT: D 28 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7146 (mm-30) REVERT: E 43 ILE cc_start: 0.8924 (pt) cc_final: 0.8711 (pt) REVERT: F 193 HIS cc_start: 0.7965 (p-80) cc_final: 0.7571 (p-80) REVERT: J 356 ILE cc_start: 0.9038 (mt) cc_final: 0.8733 (mp) REVERT: J 390 CYS cc_start: 0.6584 (m) cc_final: 0.6128 (t) REVERT: R 21 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.6578 (mmm160) REVERT: S 184 MET cc_start: 0.6585 (ttm) cc_final: 0.6328 (ttm) REVERT: S 228 ARG cc_start: 0.3559 (mtt-85) cc_final: 0.3315 (mtp85) REVERT: S 256 VAL cc_start: 0.6193 (m) cc_final: 0.5901 (m) REVERT: S 266 LYS cc_start: 0.6712 (tttm) cc_final: 0.6208 (tptm) outliers start: 10 outliers final: 2 residues processed: 658 average time/residue: 0.4082 time to fit residues: 402.3832 Evaluate side-chains 351 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 348 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain G residue 263 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 296 optimal weight: 0.0040 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN B 43 ASN B 140 HIS B 218 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 442 ASN C 235 GLN C 360 ASN C 368 GLN C 394 HIS C 439 GLN C 442 ASN D 27 ASN D 30 ASN E 30 ASN F 137 ASN F 203 HIS G 125 HIS G 235 GLN G 264 ASN G 304 ASN G 349 GLN G 360 ASN G 394 HIS G 439 GLN ** G 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN H 30 ASN J 256 HIS J 353 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 152 GLN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 HIS R 405 ASN T 37 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26433 Z= 0.274 Angle : 0.643 9.426 35976 Z= 0.335 Chirality : 0.046 0.246 3987 Planarity : 0.006 0.086 4647 Dihedral : 6.111 73.259 3609 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 2.59 % Allowed : 7.93 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.14), residues: 3306 helix: -0.47 (0.24), residues: 438 sheet: -1.29 (0.16), residues: 951 loop : -1.87 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J 236 HIS 0.008 0.001 HIS B 140 PHE 0.021 0.002 PHE A 148 TYR 0.022 0.002 TYR C 308 ARG 0.006 0.001 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 379 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6262 (m-80) cc_final: 0.5832 (m-80) REVERT: B 160 LYS cc_start: 0.7639 (tppt) cc_final: 0.7438 (tppt) REVERT: C 354 ILE cc_start: 0.8340 (pt) cc_final: 0.8003 (mt) REVERT: D 28 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7140 (mm-30) REVERT: J 356 ILE cc_start: 0.9027 (mt) cc_final: 0.8782 (mp) REVERT: J 390 CYS cc_start: 0.6606 (m) cc_final: 0.6207 (t) REVERT: Q 360 TYR cc_start: 0.8088 (t80) cc_final: 0.7088 (t80) REVERT: R 88 ARG cc_start: 0.6181 (mmt180) cc_final: 0.5825 (mmt90) REVERT: S 184 MET cc_start: 0.6236 (ttm) cc_final: 0.5904 (ttt) REVERT: S 189 PHE cc_start: 0.4174 (m-80) cc_final: 0.3953 (m-10) outliers start: 73 outliers final: 43 residues processed: 422 average time/residue: 0.3854 time to fit residues: 251.1011 Evaluate side-chains 361 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 318 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 206 LYS Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 238 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 441 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 225 GLN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26433 Z= 0.253 Angle : 0.599 8.799 35976 Z= 0.312 Chirality : 0.045 0.326 3987 Planarity : 0.005 0.090 4647 Dihedral : 5.801 75.296 3608 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 2.76 % Allowed : 10.49 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3306 helix: 0.43 (0.26), residues: 438 sheet: -0.95 (0.16), residues: 1026 loop : -1.62 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP J 236 HIS 0.007 0.001 HIS R 156 PHE 0.016 0.002 PHE A 189 TYR 0.020 0.002 TYR C 373 ARG 0.007 0.001 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 334 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: A 200 TYR cc_start: 0.6570 (m-80) cc_final: 0.6081 (m-80) REVERT: B 160 LYS cc_start: 0.7684 (tppt) cc_final: 0.7319 (tppt) REVERT: C 151 GLU cc_start: 0.7751 (pm20) cc_final: 0.7473 (pm20) REVERT: C 354 ILE cc_start: 0.8415 (pt) cc_final: 0.8074 (mt) REVERT: F 118 MET cc_start: 0.6418 (tmm) cc_final: 0.6084 (tmm) REVERT: F 119 VAL cc_start: 0.7713 (t) cc_final: 0.7319 (p) REVERT: F 176 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6968 (pt0) REVERT: J 356 ILE cc_start: 0.9012 (mt) cc_final: 0.8774 (mp) REVERT: J 390 CYS cc_start: 0.6621 (m) cc_final: 0.6168 (t) REVERT: P 6 MET cc_start: 0.4964 (tpp) cc_final: 0.4560 (ttp) REVERT: Q 360 TYR cc_start: 0.8125 (t80) cc_final: 0.7135 (t80) REVERT: R 88 ARG cc_start: 0.6251 (mmt180) cc_final: 0.5832 (mmt90) REVERT: R 110 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8081 (mm) REVERT: S 184 MET cc_start: 0.6096 (ttm) cc_final: 0.5814 (ttt) REVERT: T 6 MET cc_start: 0.5240 (mpp) cc_final: 0.4601 (mmm) outliers start: 78 outliers final: 54 residues processed: 384 average time/residue: 0.3726 time to fit residues: 225.1184 Evaluate side-chains 354 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 298 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 9.9990 chunk 223 optimal weight: 40.0000 chunk 154 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 chunk 316 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 282 optimal weight: 0.3980 chunk 85 optimal weight: 0.0270 overall best weight: 2.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN C 439 GLN J 232 GLN Q 132 ASN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 225 GLN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 353 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26433 Z= 0.200 Angle : 0.573 10.106 35976 Z= 0.297 Chirality : 0.044 0.304 3987 Planarity : 0.005 0.073 4647 Dihedral : 5.606 76.104 3608 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.59 % Rotamer: Outliers : 2.94 % Allowed : 11.16 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -1.32 (0.14), residues: 3306 helix: 0.86 (0.26), residues: 438 sheet: -0.68 (0.16), residues: 1023 loop : -1.43 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP J 236 HIS 0.005 0.001 HIS R 156 PHE 0.021 0.001 PHE A 189 TYR 0.026 0.001 TYR C 373 ARG 0.005 0.000 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 317 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7072 (m-30) REVERT: A 200 TYR cc_start: 0.6790 (m-80) cc_final: 0.6216 (m-80) REVERT: A 214 PHE cc_start: 0.6292 (m-10) cc_final: 0.6079 (m-80) REVERT: C 354 ILE cc_start: 0.8485 (pt) cc_final: 0.8137 (mt) REVERT: F 193 HIS cc_start: 0.8068 (p-80) cc_final: 0.7736 (p-80) REVERT: F 254 SER cc_start: 0.7425 (p) cc_final: 0.7158 (m) REVERT: G 97 ASP cc_start: 0.7389 (p0) cc_final: 0.7106 (p0) REVERT: G 377 LYS cc_start: 0.8205 (tttm) cc_final: 0.7829 (ptpp) REVERT: J 356 ILE cc_start: 0.8985 (mt) cc_final: 0.8759 (mp) REVERT: J 390 CYS cc_start: 0.6629 (m) cc_final: 0.6162 (t) REVERT: Q 239 ASN cc_start: 0.7937 (t0) cc_final: 0.7247 (t0) REVERT: Q 255 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7705 (mt) REVERT: Q 357 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7707 (p) REVERT: Q 360 TYR cc_start: 0.8177 (t80) cc_final: 0.7195 (t80) REVERT: R 88 ARG cc_start: 0.6273 (mmt180) cc_final: 0.5864 (mmt90) REVERT: S 184 MET cc_start: 0.5855 (ttm) cc_final: 0.5559 (ttt) outliers start: 83 outliers final: 62 residues processed: 371 average time/residue: 0.3741 time to fit residues: 217.8182 Evaluate side-chains 359 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 294 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 225 GLN Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 20.0000 chunk 179 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 269 optimal weight: 10.0000 chunk 218 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 161 optimal weight: 20.0000 chunk 283 optimal weight: 4.9990 chunk 79 optimal weight: 0.0050 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN J 80 HIS J 81 GLN J 358 HIS Q 91 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26433 Z= 0.278 Angle : 0.592 9.450 35976 Z= 0.307 Chirality : 0.045 0.333 3987 Planarity : 0.005 0.104 4647 Dihedral : 5.634 77.452 3608 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.04 % Rotamer: Outliers : 3.33 % Allowed : 11.51 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -1.14 (0.15), residues: 3306 helix: 1.09 (0.27), residues: 438 sheet: -0.60 (0.16), residues: 1038 loop : -1.32 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP J 236 HIS 0.009 0.001 HIS C 230 PHE 0.018 0.002 PHE A 189 TYR 0.019 0.002 TYR C 308 ARG 0.008 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 314 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: A 200 TYR cc_start: 0.6796 (m-80) cc_final: 0.6320 (m-80) REVERT: C 354 ILE cc_start: 0.8504 (pt) cc_final: 0.8141 (mt) REVERT: F 193 HIS cc_start: 0.8089 (p-80) cc_final: 0.7751 (p-80) REVERT: F 254 SER cc_start: 0.7474 (p) cc_final: 0.7209 (m) REVERT: G 377 LYS cc_start: 0.8194 (tttm) cc_final: 0.7820 (ptpp) REVERT: J 356 ILE cc_start: 0.8992 (mt) cc_final: 0.8785 (mp) REVERT: J 390 CYS cc_start: 0.6734 (m) cc_final: 0.6139 (t) REVERT: Q 255 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7677 (mt) REVERT: Q 357 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7722 (p) REVERT: Q 360 TYR cc_start: 0.8152 (t80) cc_final: 0.7391 (t80) REVERT: R 88 ARG cc_start: 0.6296 (mmt180) cc_final: 0.5865 (mmt90) REVERT: S 184 MET cc_start: 0.5851 (ttm) cc_final: 0.5580 (ttt) outliers start: 94 outliers final: 74 residues processed: 377 average time/residue: 0.3679 time to fit residues: 218.1808 Evaluate side-chains 366 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 289 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 302 ASP Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Q residue 412 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 225 GLN Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 146 LYS Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 0.8980 chunk 284 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 316 optimal weight: 0.3980 chunk 262 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN J 81 GLN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26433 Z= 0.195 Angle : 0.557 10.314 35976 Z= 0.288 Chirality : 0.044 0.329 3987 Planarity : 0.004 0.071 4647 Dihedral : 5.418 77.881 3608 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.17 % Favored : 94.68 % Rotamer: Outliers : 2.80 % Allowed : 12.72 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -0.89 (0.15), residues: 3306 helix: 1.25 (0.27), residues: 438 sheet: -0.36 (0.16), residues: 1014 loop : -1.19 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP J 236 HIS 0.005 0.001 HIS C 230 PHE 0.011 0.001 PHE J 217 TYR 0.017 0.001 TYR C 308 ARG 0.005 0.000 ARG Q 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 312 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: A 200 TYR cc_start: 0.6759 (m-80) cc_final: 0.6443 (m-80) REVERT: C 354 ILE cc_start: 0.8556 (pt) cc_final: 0.8181 (mt) REVERT: F 118 MET cc_start: 0.6512 (tmm) cc_final: 0.6297 (tmm) REVERT: F 193 HIS cc_start: 0.8058 (p-80) cc_final: 0.7734 (p-80) REVERT: F 254 SER cc_start: 0.7522 (p) cc_final: 0.7250 (m) REVERT: G 377 LYS cc_start: 0.8132 (tttm) cc_final: 0.7828 (ptpp) REVERT: J 390 CYS cc_start: 0.6722 (m) cc_final: 0.6129 (t) REVERT: Q 160 ASN cc_start: 0.6172 (t0) cc_final: 0.5972 (t0) REVERT: Q 360 TYR cc_start: 0.8176 (t80) cc_final: 0.7219 (t80) REVERT: R 88 ARG cc_start: 0.6318 (mmt180) cc_final: 0.5901 (mmt90) REVERT: S 184 MET cc_start: 0.6434 (ttm) cc_final: 0.6074 (ttt) outliers start: 79 outliers final: 66 residues processed: 360 average time/residue: 0.3660 time to fit residues: 208.9934 Evaluate side-chains 353 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 286 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 302 ASP Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 0.4980 chunk 35 optimal weight: 0.0570 chunk 180 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 315 optimal weight: 30.0000 chunk 197 optimal weight: 0.0070 chunk 192 optimal weight: 8.9990 chunk 145 optimal weight: 0.0470 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN J 358 HIS ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26433 Z= 0.123 Angle : 0.534 9.345 35976 Z= 0.274 Chirality : 0.043 0.434 3987 Planarity : 0.004 0.071 4647 Dihedral : 5.095 78.193 3608 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.72 % Favored : 95.13 % Rotamer: Outliers : 2.16 % Allowed : 13.82 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: 3306 helix: 1.40 (0.27), residues: 438 sheet: -0.09 (0.16), residues: 1014 loop : -1.04 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP J 236 HIS 0.006 0.001 HIS J 353 PHE 0.024 0.001 PHE J 217 TYR 0.026 0.001 TYR A 177 ARG 0.006 0.000 ARG Q 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 325 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6817 (m-80) cc_final: 0.6382 (m-80) REVERT: B 247 LYS cc_start: 0.7118 (mtpt) cc_final: 0.6855 (ttpt) REVERT: C 354 ILE cc_start: 0.8503 (pt) cc_final: 0.8075 (mt) REVERT: E 36 MET cc_start: 0.7702 (ttt) cc_final: 0.7463 (ttt) REVERT: F 152 HIS cc_start: 0.7751 (p-80) cc_final: 0.7488 (p-80) REVERT: F 193 HIS cc_start: 0.7956 (p-80) cc_final: 0.7657 (p-80) REVERT: F 254 SER cc_start: 0.7503 (p) cc_final: 0.7285 (m) REVERT: G 377 LYS cc_start: 0.8144 (tttm) cc_final: 0.7890 (ptpp) REVERT: J 390 CYS cc_start: 0.6683 (m) cc_final: 0.6104 (t) REVERT: J 401 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.7924 (mtp85) REVERT: P 33 MET cc_start: 0.7586 (ttp) cc_final: 0.7113 (ptm) REVERT: Q 160 ASN cc_start: 0.6006 (t0) cc_final: 0.5762 (t0) REVERT: Q 360 TYR cc_start: 0.8165 (t80) cc_final: 0.7159 (t80) REVERT: R 88 ARG cc_start: 0.6112 (mmt180) cc_final: 0.5717 (mmt90) REVERT: R 398 THR cc_start: 0.7176 (m) cc_final: 0.6785 (m) REVERT: S 184 MET cc_start: 0.6497 (ttm) cc_final: 0.6139 (ttt) outliers start: 61 outliers final: 35 residues processed: 364 average time/residue: 0.3979 time to fit residues: 229.3425 Evaluate side-chains 322 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 287 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 225 GLN Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 HIS J 358 HIS ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 26433 Z= 0.436 Angle : 0.666 9.563 35976 Z= 0.345 Chirality : 0.049 0.433 3987 Planarity : 0.005 0.072 4647 Dihedral : 5.770 80.650 3608 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.29 % Favored : 93.56 % Rotamer: Outliers : 2.55 % Allowed : 13.67 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -0.82 (0.15), residues: 3306 helix: 1.30 (0.27), residues: 435 sheet: -0.33 (0.16), residues: 1062 loop : -1.14 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP J 236 HIS 0.014 0.002 HIS C 230 PHE 0.023 0.002 PHE Q 259 TYR 0.025 0.002 TYR A 177 ARG 0.008 0.001 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 294 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6981 (m-80) cc_final: 0.6657 (m-80) REVERT: B 160 LYS cc_start: 0.7833 (tttp) cc_final: 0.7507 (tttm) REVERT: C 354 ILE cc_start: 0.8620 (pt) cc_final: 0.8150 (mt) REVERT: F 148 PHE cc_start: 0.8311 (m-10) cc_final: 0.8108 (m-10) REVERT: F 193 HIS cc_start: 0.8133 (p-80) cc_final: 0.7807 (p-80) REVERT: G 377 LYS cc_start: 0.8165 (tttm) cc_final: 0.7836 (ptpp) REVERT: J 401 ARG cc_start: 0.8410 (mtt-85) cc_final: 0.7855 (mtp180) REVERT: P 33 MET cc_start: 0.7588 (ttp) cc_final: 0.7099 (ptm) REVERT: Q 360 TYR cc_start: 0.8192 (t80) cc_final: 0.7402 (t80) REVERT: R 88 ARG cc_start: 0.6470 (mmt180) cc_final: 0.5881 (mmt180) REVERT: S 184 MET cc_start: 0.6551 (ttm) cc_final: 0.6212 (ttt) outliers start: 72 outliers final: 58 residues processed: 342 average time/residue: 0.3870 time to fit residues: 210.1230 Evaluate side-chains 341 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 283 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 302 ASP Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain Q residue 192 ASP Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 225 GLN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 146 LYS Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 5.9990 chunk 275 optimal weight: 8.9990 chunk 293 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 265 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 292 optimal weight: 0.0980 chunk 192 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26433 Z= 0.201 Angle : 0.564 8.353 35976 Z= 0.291 Chirality : 0.045 0.425 3987 Planarity : 0.004 0.068 4647 Dihedral : 5.431 78.706 3608 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.72 % Favored : 95.13 % Rotamer: Outliers : 2.13 % Allowed : 14.03 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -0.63 (0.15), residues: 3306 helix: 1.38 (0.27), residues: 438 sheet: -0.17 (0.16), residues: 1038 loop : -1.01 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP J 236 HIS 0.006 0.001 HIS C 230 PHE 0.026 0.001 PHE A 189 TYR 0.024 0.001 TYR A 177 ARG 0.003 0.000 ARG Q 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 289 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6987 (m-80) cc_final: 0.6619 (m-80) REVERT: B 160 LYS cc_start: 0.7990 (tttp) cc_final: 0.7660 (tmtm) REVERT: C 300 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: C 354 ILE cc_start: 0.8585 (pt) cc_final: 0.8238 (mt) REVERT: F 193 HIS cc_start: 0.8093 (p-80) cc_final: 0.7788 (p-80) REVERT: F 254 SER cc_start: 0.7649 (p) cc_final: 0.7377 (m) REVERT: J 390 CYS cc_start: 0.7012 (m) cc_final: 0.6308 (t) REVERT: J 401 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.7883 (mtp180) REVERT: P 33 MET cc_start: 0.7450 (ttp) cc_final: 0.6945 (ptm) REVERT: Q 360 TYR cc_start: 0.8201 (t80) cc_final: 0.7249 (t80) REVERT: R 88 ARG cc_start: 0.6332 (mmt180) cc_final: 0.5923 (mmt90) REVERT: S 184 MET cc_start: 0.6539 (ttm) cc_final: 0.6184 (ttt) outliers start: 60 outliers final: 53 residues processed: 331 average time/residue: 0.3658 time to fit residues: 191.9507 Evaluate side-chains 343 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 289 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 302 ASP Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 192 ASP Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 225 GLN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain S residue 146 LYS Chi-restraints excluded: chain S residue 189 PHE Chi-restraints excluded: chain S residue 251 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 chunk 299 optimal weight: 0.3980 chunk 259 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 159 optimal weight: 0.0980 chunk 206 optimal weight: 4.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN R 160 ASN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26433 Z= 0.245 Angle : 0.582 8.161 35976 Z= 0.300 Chirality : 0.045 0.406 3987 Planarity : 0.005 0.071 4647 Dihedral : 5.421 78.537 3608 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 2.27 % Allowed : 14.20 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -0.60 (0.15), residues: 3306 helix: 1.40 (0.27), residues: 438 sheet: -0.16 (0.16), residues: 1041 loop : -0.98 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP J 236 HIS 0.008 0.001 HIS C 230 PHE 0.013 0.002 PHE J 328 TYR 0.022 0.002 TYR A 177 ARG 0.004 0.000 ARG Q 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 294 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6988 (m-80) cc_final: 0.6638 (m-80) REVERT: C 300 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7082 (pt0) REVERT: C 354 ILE cc_start: 0.8562 (pt) cc_final: 0.8206 (mt) REVERT: F 193 HIS cc_start: 0.8110 (p-80) cc_final: 0.7807 (p-80) REVERT: F 254 SER cc_start: 0.7618 (p) cc_final: 0.7386 (m) REVERT: J 401 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.7895 (mtp180) REVERT: P 33 MET cc_start: 0.7463 (ttp) cc_final: 0.6956 (ptm) REVERT: Q 360 TYR cc_start: 0.8210 (t80) cc_final: 0.7248 (t80) REVERT: R 88 ARG cc_start: 0.6366 (mmt180) cc_final: 0.5933 (mmt90) REVERT: S 184 MET cc_start: 0.6557 (ttm) cc_final: 0.6203 (ttt) outliers start: 64 outliers final: 57 residues processed: 337 average time/residue: 0.3679 time to fit residues: 196.1913 Evaluate side-chains 345 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 287 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 302 ASP Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 396 CYS Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 192 ASP Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 212 ASN Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 390 CYS Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 225 GLN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 146 LYS Chi-restraints excluded: chain S residue 189 PHE Chi-restraints excluded: chain S residue 251 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.160124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118561 restraints weight = 37487.781| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.62 r_work: 0.3139 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26433 Z= 0.264 Angle : 0.590 8.324 35976 Z= 0.304 Chirality : 0.045 0.408 3987 Planarity : 0.005 0.069 4647 Dihedral : 5.439 78.502 3608 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.44 % Favored : 94.40 % Rotamer: Outliers : 2.44 % Allowed : 14.17 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % 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: -0.59 (0.15), residues: 3306 helix: 1.38 (0.27), residues: 438 sheet: -0.16 (0.16), residues: 1056 loop : -0.96 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP J 236 HIS 0.008 0.001 HIS C 230 PHE 0.013 0.002 PHE Q 259 TYR 0.021 0.002 TYR A 177 ARG 0.003 0.000 ARG Q 230 =============================================================================== Job complete usr+sys time: 6270.02 seconds wall clock time: 114 minutes 10.92 seconds (6850.92 seconds total)