Starting phenix.real_space_refine on Fri Mar 15 04:11:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/03_2024/8f0k_28759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/03_2024/8f0k_28759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/03_2024/8f0k_28759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/03_2024/8f0k_28759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/03_2024/8f0k_28759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/03_2024/8f0k_28759.pdb" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 P 2 5.49 5 S 78 5.16 5 C 6760 2.51 5 N 1761 2.21 5 O 1952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 36": "NH1" <-> "NH2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R GLU 334": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10553 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 280 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Chain: "R" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3046 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1888 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 358 Unusual residues: {'NAG': 3, 'P42': 1, 'PLM': 8, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.07, per 1000 atoms: 0.58 Number of scatterers: 10553 At special positions: 0 Unit cell: (99.125, 168.188, 93.4375, 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) S 78 16.00 P 2 15.00 O 1952 8.00 N 1761 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 82 " distance=2.04 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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 Links applied NAG-ASN " NAG E 201 " - " ASN E 29 " " NAG E 202 " - " ASN E 71 " " NAG R 501 " - " ASN R 125 " " NAG R 502 " - " ASN R 130 " " NAG R 503 " - " ASN R 73 " Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.7 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 13 sheets defined 45.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'E' and resid 29 through 48 Proline residue: E 38 - end of helix Processing helix chain 'E' and resid 52 through 57 removed outlier: 4.249A pdb=" N CYS E 57 " --> pdb=" O TRP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 80 removed outlier: 4.287A pdb=" N PHE E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 120 through 141 Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 removed outlier: 3.765A pdb=" N HIS P 18 " --> pdb=" O ASN P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 24 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 131 through 135 Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.539A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.565A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.944A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 removed outlier: 3.512A pdb=" N LYS R 340 " --> pdb=" O HIS R 336 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 406 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.537A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.624A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.893A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.653A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.434A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.973A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.560A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.800A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.276A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.583A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.507A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.748A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.172A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1488 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: 3.08 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1724 1.32 - 1.45: 2934 1.45 - 1.57: 5975 1.57 - 1.70: 4 1.70 - 1.82: 112 Bond restraints: 10749 Sorted by residual: bond pdb=" N VAL R 250 " pdb=" CA VAL R 250 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.17e-02 7.31e+03 9.72e+00 bond pdb=" N THR R 254 " pdb=" CA THR R 254 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.19e-02 7.06e+03 8.34e+00 bond pdb=" N VAL E 79 " pdb=" CA VAL E 79 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.29e+00 bond pdb=" N GLU R 255 " pdb=" CA GLU R 255 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.25e+00 bond pdb=" N VAL R 249 " pdb=" CA VAL R 249 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.42e+00 ... (remaining 10744 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.93: 217 105.93 - 113.00: 5680 113.00 - 120.06: 3856 120.06 - 127.13: 4633 127.13 - 134.19: 130 Bond angle restraints: 14516 Sorted by residual: angle pdb=" N VAL R 250 " pdb=" CA VAL R 250 " pdb=" C VAL R 250 " ideal model delta sigma weight residual 110.42 116.66 -6.24 9.60e-01 1.09e+00 4.22e+01 angle pdb=" N PHE R 253 " pdb=" CA PHE R 253 " pdb=" C PHE R 253 " ideal model delta sigma weight residual 111.36 116.89 -5.53 1.09e+00 8.42e-01 2.58e+01 angle pdb=" C PHE R 172 " pdb=" CA PHE R 172 " pdb=" CB PHE R 172 " ideal model delta sigma weight residual 110.90 103.34 7.56 1.58e+00 4.01e-01 2.29e+01 angle pdb=" C ASN E 86 " pdb=" CA ASN E 86 " pdb=" CB ASN E 86 " ideal model delta sigma weight residual 108.87 115.57 -6.70 1.55e+00 4.16e-01 1.87e+01 angle pdb=" CA VAL R 171 " pdb=" C VAL R 171 " pdb=" O VAL R 171 " ideal model delta sigma weight residual 121.05 116.38 4.67 1.11e+00 8.12e-01 1.77e+01 ... (remaining 14511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 6282 25.31 - 50.63: 261 50.63 - 75.94: 47 75.94 - 101.25: 11 101.25 - 126.57: 6 Dihedral angle restraints: 6607 sinusoidal: 2904 harmonic: 3703 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -145.39 59.39 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 129.21 -36.21 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" N1 PTY R 514 " pdb=" C2 PTY R 514 " pdb=" C3 PTY R 514 " pdb=" O11 PTY R 514 " ideal model delta sinusoidal sigma weight residual 65.33 -61.24 126.57 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 6604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1341 0.053 - 0.106: 193 0.106 - 0.159: 46 0.159 - 0.212: 10 0.212 - 0.265: 4 Chirality restraints: 1594 Sorted by residual: chirality pdb=" C6 PTY R 514 " pdb=" C1 PTY R 514 " pdb=" C5 PTY R 514 " pdb=" O7 PTY R 514 " both_signs ideal model delta sigma weight residual False 2.49 2.22 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ARG R 258 " pdb=" N ARG R 258 " pdb=" C ARG R 258 " pdb=" CB ARG R 258 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE R 172 " pdb=" N PHE R 172 " pdb=" C PHE R 172 " pdb=" CB PHE R 172 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1591 not shown) Planarity restraints: 1821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 202 " -0.328 2.00e-02 2.50e+03 2.76e-01 9.50e+02 pdb=" C7 NAG E 202 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG E 202 " -0.196 2.00e-02 2.50e+03 pdb=" N2 NAG E 202 " 0.474 2.00e-02 2.50e+03 pdb=" O7 NAG E 202 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 170 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C PHE R 170 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE R 170 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL R 171 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 175 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C SER R 175 " -0.041 2.00e-02 2.50e+03 pdb=" O SER R 175 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU R 176 " 0.014 2.00e-02 2.50e+03 ... (remaining 1818 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2322 2.78 - 3.31: 9812 3.31 - 3.84: 17739 3.84 - 4.37: 21830 4.37 - 4.90: 36870 Nonbonded interactions: 88573 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.252 2.440 nonbonded pdb=" CD GLU R 397 " pdb=" O HOH R 602 " model vdw 2.274 3.270 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.304 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR A 204 " pdb=" N SER A 205 " model vdw 2.319 2.520 ... (remaining 88568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.770 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.780 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 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 : 0.004 0.051 10749 Z= 0.255 Angle : 0.594 9.660 14516 Z= 0.367 Chirality : 0.044 0.265 1594 Planarity : 0.007 0.276 1816 Dihedral : 14.281 126.565 4187 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.91 % Allowed : 9.83 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1254 helix: -1.82 (0.16), residues: 509 sheet: -0.24 (0.32), residues: 232 loop : -0.54 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.002 0.000 HIS R 381 PHE 0.007 0.001 PHE B 199 TYR 0.019 0.001 TYR E 83 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 VAL cc_start: 0.6974 (m) cc_final: 0.6758 (t) REVERT: E 133 MET cc_start: 0.5509 (mmm) cc_final: 0.5080 (mpm) REVERT: R 195 SER cc_start: 0.6745 (m) cc_final: 0.6315 (p) REVERT: R 225 PHE cc_start: 0.6191 (m-80) cc_final: 0.5886 (m-80) REVERT: R 314 PHE cc_start: 0.6289 (m-10) cc_final: 0.5874 (t80) REVERT: R 395 ASN cc_start: 0.6176 (t0) cc_final: 0.5832 (t0) REVERT: A 20 ARG cc_start: 0.6216 (mtm110) cc_final: 0.5755 (ttm110) REVERT: A 28 LYS cc_start: 0.7034 (ttpp) cc_final: 0.6807 (ttpp) REVERT: A 296 LEU cc_start: 0.6834 (mp) cc_final: 0.6507 (mt) REVERT: A 299 GLU cc_start: 0.5464 (mt-10) cc_final: 0.5250 (mt-10) REVERT: A 344 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 45 MET cc_start: 0.7865 (mtt) cc_final: 0.7589 (mtm) REVERT: B 188 MET cc_start: 0.8426 (mmm) cc_final: 0.8151 (mmm) REVERT: G 21 MET cc_start: 0.5616 (mmm) cc_final: 0.5138 (mpm) REVERT: G 25 ILE cc_start: 0.6224 (pt) cc_final: 0.5892 (pt) REVERT: N 1 GLN cc_start: 0.6078 (tp-100) cc_final: 0.5826 (mm-40) REVERT: N 73 ASP cc_start: 0.7681 (t0) cc_final: 0.7410 (t0) outliers start: 10 outliers final: 2 residues processed: 218 average time/residue: 1.5114 time to fit residues: 349.3957 Evaluate side-chains 156 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 ASN E 103 ASN P 22 ASN P 31 ASN P 35 ASN R 184 HIS R 201 HIS R 223 HIS R 399 GLN A 14 ASN A 54 ASN A 59 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 387 HIS A 390 GLN B 9 GLN B 17 GLN B 88 ASN B 175 GLN B 293 ASN N 84 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10749 Z= 0.333 Angle : 0.756 10.287 14516 Z= 0.404 Chirality : 0.049 0.184 1594 Planarity : 0.006 0.059 1816 Dihedral : 12.151 135.984 1838 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.73 % Allowed : 10.74 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1254 helix: 0.78 (0.21), residues: 521 sheet: -0.05 (0.32), residues: 245 loop : 0.06 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 234 HIS 0.012 0.003 HIS R 336 PHE 0.021 0.003 PHE N 29 TYR 0.019 0.003 TYR R 391 ARG 0.009 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ARG cc_start: 0.4851 (OUTLIER) cc_final: 0.4460 (mtm180) REVERT: R 179 GLN cc_start: 0.7114 (mt0) cc_final: 0.6890 (mt0) REVERT: R 195 SER cc_start: 0.6926 (m) cc_final: 0.6580 (p) REVERT: R 314 PHE cc_start: 0.6346 (m-80) cc_final: 0.5757 (t80) REVERT: R 340 LYS cc_start: 0.5188 (OUTLIER) cc_final: 0.4829 (mtpt) REVERT: A 20 ARG cc_start: 0.6293 (mtm110) cc_final: 0.5823 (ttm110) REVERT: A 28 LYS cc_start: 0.7241 (ttpp) cc_final: 0.6882 (ttpp) REVERT: A 265 ARG cc_start: 0.6860 (ptt-90) cc_final: 0.6254 (ppt90) REVERT: A 296 LEU cc_start: 0.7097 (mp) cc_final: 0.6752 (mt) REVERT: B 45 MET cc_start: 0.7999 (mtt) cc_final: 0.7527 (mtm) REVERT: B 217 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6217 (pmm) REVERT: G 21 MET cc_start: 0.5526 (mmm) cc_final: 0.5261 (mpt) REVERT: N 1 GLN cc_start: 0.6184 (tp-100) cc_final: 0.5893 (mm-40) outliers start: 30 outliers final: 9 residues processed: 171 average time/residue: 1.5007 time to fit residues: 273.1083 Evaluate side-chains 150 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 0.0980 chunk 30 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 395 ASN R 396 ASN A 12 GLN A 213 GLN A 357 HIS A 390 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10749 Z= 0.189 Angle : 0.583 6.739 14516 Z= 0.312 Chirality : 0.043 0.148 1594 Planarity : 0.004 0.037 1816 Dihedral : 11.502 130.437 1837 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.82 % Allowed : 11.83 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1254 helix: 1.63 (0.22), residues: 520 sheet: 0.02 (0.32), residues: 235 loop : 0.25 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 234 HIS 0.007 0.001 HIS R 336 PHE 0.021 0.002 PHE E 44 TYR 0.010 0.001 TYR A 339 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: R 174 ARG cc_start: 0.4836 (OUTLIER) cc_final: 0.4380 (mtm180) REVERT: R 179 GLN cc_start: 0.7052 (mt0) cc_final: 0.6795 (mt0) REVERT: R 195 SER cc_start: 0.6988 (m) cc_final: 0.6595 (p) REVERT: R 314 PHE cc_start: 0.6323 (m-80) cc_final: 0.5731 (t80) REVERT: A 20 ARG cc_start: 0.6284 (mtm110) cc_final: 0.5903 (ttp-110) REVERT: A 28 LYS cc_start: 0.7167 (ttpp) cc_final: 0.6872 (ttpp) REVERT: A 265 ARG cc_start: 0.6812 (ptt-90) cc_final: 0.6252 (ppt90) REVERT: A 296 LEU cc_start: 0.7041 (mp) cc_final: 0.6690 (mt) REVERT: G 21 MET cc_start: 0.5420 (mmm) cc_final: 0.5136 (mpt) REVERT: G 29 LYS cc_start: 0.7589 (mmtm) cc_final: 0.7373 (mmtm) REVERT: N 1 GLN cc_start: 0.6190 (tp-100) cc_final: 0.5870 (mm-40) REVERT: N 73 ASP cc_start: 0.7941 (t0) cc_final: 0.7739 (t0) outliers start: 20 outliers final: 6 residues processed: 158 average time/residue: 1.5506 time to fit residues: 259.5526 Evaluate side-chains 147 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 10.0000 chunk 57 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 0.1980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS A 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10749 Z= 0.132 Angle : 0.493 6.612 14516 Z= 0.261 Chirality : 0.040 0.140 1594 Planarity : 0.003 0.039 1816 Dihedral : 10.532 115.433 1837 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.36 % Allowed : 12.56 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1254 helix: 2.07 (0.23), residues: 521 sheet: 0.10 (0.32), residues: 232 loop : 0.46 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR R 191 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: 0.0476 (ptm) cc_final: 0.0107 (tpt) REVERT: R 169 ILE cc_start: 0.6495 (mt) cc_final: 0.6107 (mm) REVERT: R 174 ARG cc_start: 0.4750 (OUTLIER) cc_final: 0.4268 (mtm180) REVERT: R 195 SER cc_start: 0.6969 (m) cc_final: 0.6577 (p) REVERT: R 314 PHE cc_start: 0.6323 (m-80) cc_final: 0.5788 (t80) REVERT: R 340 LYS cc_start: 0.5105 (mtmm) cc_final: 0.4849 (mppt) REVERT: A 16 GLU cc_start: 0.5209 (tp30) cc_final: 0.4468 (tp30) REVERT: A 17 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5311 (mtpt) REVERT: A 20 ARG cc_start: 0.6239 (mtm110) cc_final: 0.5726 (ttm110) REVERT: A 28 LYS cc_start: 0.7138 (ttpp) cc_final: 0.6837 (ttpp) REVERT: A 265 ARG cc_start: 0.6794 (ptt-90) cc_final: 0.6216 (ppt90) REVERT: A 296 LEU cc_start: 0.6990 (mp) cc_final: 0.6634 (mt) REVERT: B 23 LYS cc_start: 0.6689 (tmtt) cc_final: 0.6430 (ttmt) REVERT: B 61 MET cc_start: 0.8541 (ppp) cc_final: 0.8337 (ppp) REVERT: G 21 MET cc_start: 0.5398 (mmm) cc_final: 0.5127 (mpt) REVERT: N 1 GLN cc_start: 0.6170 (tp-100) cc_final: 0.5891 (mm-40) REVERT: N 73 ASP cc_start: 0.7931 (t0) cc_final: 0.7701 (t0) outliers start: 15 outliers final: 5 residues processed: 158 average time/residue: 1.5990 time to fit residues: 267.3706 Evaluate side-chains 151 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10749 Z= 0.202 Angle : 0.592 7.670 14516 Z= 0.314 Chirality : 0.043 0.176 1594 Planarity : 0.004 0.037 1816 Dihedral : 11.026 126.930 1837 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.00 % Allowed : 12.37 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1254 helix: 2.06 (0.23), residues: 520 sheet: -0.01 (0.33), residues: 233 loop : 0.47 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 234 HIS 0.005 0.001 HIS R 336 PHE 0.017 0.002 PHE A 212 TYR 0.010 0.002 TYR N 117 ARG 0.003 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0420 (ptm) cc_final: 0.0032 (tpp) REVERT: R 169 ILE cc_start: 0.6541 (mt) cc_final: 0.6163 (mm) REVERT: R 174 ARG cc_start: 0.4741 (OUTLIER) cc_final: 0.4296 (mtm180) REVERT: R 195 SER cc_start: 0.7057 (m) cc_final: 0.6607 (p) REVERT: R 260 ARG cc_start: 0.5462 (ptp-170) cc_final: 0.5073 (ptp-170) REVERT: R 314 PHE cc_start: 0.6363 (m-80) cc_final: 0.5748 (t80) REVERT: R 340 LYS cc_start: 0.5181 (mtmm) cc_final: 0.4872 (mppt) REVERT: A 16 GLU cc_start: 0.5316 (tp30) cc_final: 0.4568 (tp30) REVERT: A 20 ARG cc_start: 0.6247 (mtm110) cc_final: 0.5872 (ttm110) REVERT: A 28 LYS cc_start: 0.7181 (ttpp) cc_final: 0.6852 (ttpp) REVERT: A 265 ARG cc_start: 0.6790 (ptt-90) cc_final: 0.6170 (ppt90) REVERT: A 296 LEU cc_start: 0.7069 (mp) cc_final: 0.6701 (mt) REVERT: B 217 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6301 (pmm) REVERT: G 21 MET cc_start: 0.5415 (mmm) cc_final: 0.5149 (mpt) REVERT: N 1 GLN cc_start: 0.6169 (tp-100) cc_final: 0.5850 (mm-40) outliers start: 22 outliers final: 10 residues processed: 155 average time/residue: 1.5964 time to fit residues: 262.0317 Evaluate side-chains 148 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS A 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10749 Z= 0.148 Angle : 0.525 8.988 14516 Z= 0.277 Chirality : 0.041 0.167 1594 Planarity : 0.003 0.039 1816 Dihedral : 10.480 119.635 1837 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.82 % Allowed : 13.10 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1254 helix: 2.21 (0.23), residues: 521 sheet: 0.09 (0.33), residues: 231 loop : 0.58 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS R 277 PHE 0.015 0.001 PHE A 212 TYR 0.008 0.001 TYR N 95 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0267 (ptm) cc_final: -0.0055 (tpp) REVERT: R 48 MET cc_start: 0.0065 (mmt) cc_final: -0.0347 (tmt) REVERT: R 169 ILE cc_start: 0.6570 (mt) cc_final: 0.6127 (mm) REVERT: R 174 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.4240 (mtm180) REVERT: R 195 SER cc_start: 0.7036 (m) cc_final: 0.6600 (p) REVERT: R 260 ARG cc_start: 0.5475 (ptp-170) cc_final: 0.5093 (ptp-170) REVERT: R 314 PHE cc_start: 0.6283 (m-80) cc_final: 0.5721 (t80) REVERT: R 340 LYS cc_start: 0.5165 (mtmm) cc_final: 0.4861 (mppt) REVERT: R 376 MET cc_start: 0.6294 (mmm) cc_final: 0.6016 (tpp) REVERT: R 408 GLN cc_start: 0.3269 (OUTLIER) cc_final: 0.2966 (tt0) REVERT: A 16 GLU cc_start: 0.5328 (tp30) cc_final: 0.4577 (tp30) REVERT: A 17 LYS cc_start: 0.5696 (OUTLIER) cc_final: 0.5273 (mtpt) REVERT: A 20 ARG cc_start: 0.6253 (mtm110) cc_final: 0.5924 (ttm110) REVERT: A 28 LYS cc_start: 0.7084 (ttpp) cc_final: 0.6807 (ttpp) REVERT: A 265 ARG cc_start: 0.6762 (ptt-90) cc_final: 0.6172 (ppt90) REVERT: A 296 LEU cc_start: 0.7046 (mp) cc_final: 0.6668 (mt) REVERT: G 21 MET cc_start: 0.5416 (mmm) cc_final: 0.5139 (mpt) REVERT: N 1 GLN cc_start: 0.6168 (tp-100) cc_final: 0.5885 (mm-40) outliers start: 20 outliers final: 10 residues processed: 157 average time/residue: 1.6506 time to fit residues: 274.0163 Evaluate side-chains 151 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10749 Z= 0.162 Angle : 0.544 10.785 14516 Z= 0.287 Chirality : 0.041 0.191 1594 Planarity : 0.004 0.038 1816 Dihedral : 10.373 111.435 1837 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.91 % Allowed : 13.19 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1254 helix: 2.26 (0.23), residues: 518 sheet: 0.10 (0.33), residues: 231 loop : 0.52 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.003 0.001 HIS R 302 PHE 0.015 0.002 PHE A 212 TYR 0.010 0.001 TYR N 117 ARG 0.003 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0282 (ptm) cc_final: -0.0018 (tpp) REVERT: R 48 MET cc_start: 0.0313 (mmt) cc_final: -0.0242 (tmt) REVERT: R 167 LEU cc_start: 0.6501 (tp) cc_final: 0.6249 (tm) REVERT: R 169 ILE cc_start: 0.6541 (mt) cc_final: 0.6091 (mm) REVERT: R 174 ARG cc_start: 0.4722 (OUTLIER) cc_final: 0.4280 (mtm180) REVERT: R 195 SER cc_start: 0.7052 (m) cc_final: 0.6593 (p) REVERT: R 230 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6702 (ttm) REVERT: R 314 PHE cc_start: 0.6277 (m-80) cc_final: 0.5689 (t80) REVERT: R 376 MET cc_start: 0.6312 (mmm) cc_final: 0.6078 (tpp) REVERT: R 408 GLN cc_start: 0.3179 (OUTLIER) cc_final: 0.2867 (tt0) REVERT: A 17 LYS cc_start: 0.5688 (OUTLIER) cc_final: 0.5246 (mtpt) REVERT: A 20 ARG cc_start: 0.6261 (mtm110) cc_final: 0.5923 (ttm110) REVERT: A 28 LYS cc_start: 0.7126 (ttpp) cc_final: 0.6829 (ttpp) REVERT: A 265 ARG cc_start: 0.6770 (ptt-90) cc_final: 0.6162 (ppt90) REVERT: A 296 LEU cc_start: 0.7111 (mp) cc_final: 0.6844 (mt) REVERT: G 21 MET cc_start: 0.5406 (mmm) cc_final: 0.5139 (mpt) REVERT: G 29 LYS cc_start: 0.7598 (mmtm) cc_final: 0.7373 (mptp) REVERT: N 1 GLN cc_start: 0.6164 (tp-100) cc_final: 0.5873 (mm-40) outliers start: 21 outliers final: 9 residues processed: 154 average time/residue: 1.6357 time to fit residues: 266.2065 Evaluate side-chains 148 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10749 Z= 0.188 Angle : 0.579 10.474 14516 Z= 0.305 Chirality : 0.042 0.210 1594 Planarity : 0.004 0.038 1816 Dihedral : 10.643 104.818 1837 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.09 % Allowed : 13.19 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1254 helix: 2.17 (0.23), residues: 514 sheet: 0.01 (0.33), residues: 238 loop : 0.47 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 234 HIS 0.004 0.001 HIS R 302 PHE 0.016 0.002 PHE A 212 TYR 0.010 0.001 TYR N 117 ARG 0.003 0.000 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0230 (ptm) cc_final: -0.0090 (tpp) REVERT: R 48 MET cc_start: 0.0265 (mmt) cc_final: -0.0302 (tmt) REVERT: R 169 ILE cc_start: 0.6530 (mt) cc_final: 0.6136 (mm) REVERT: R 174 ARG cc_start: 0.4856 (OUTLIER) cc_final: 0.4459 (mtm180) REVERT: R 230 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6760 (ttm) REVERT: R 314 PHE cc_start: 0.6297 (m-80) cc_final: 0.5706 (t80) REVERT: R 408 GLN cc_start: 0.3286 (OUTLIER) cc_final: 0.2932 (tt0) REVERT: A 16 GLU cc_start: 0.5411 (tp30) cc_final: 0.4641 (tp30) REVERT: A 17 LYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5256 (mtpt) REVERT: A 20 ARG cc_start: 0.6231 (mtm110) cc_final: 0.5900 (ttp-110) REVERT: A 28 LYS cc_start: 0.7181 (ttpp) cc_final: 0.6849 (ttpp) REVERT: A 265 ARG cc_start: 0.6794 (ptt-90) cc_final: 0.6170 (ppt90) REVERT: B 214 ARG cc_start: 0.6565 (mtm180) cc_final: 0.6354 (mtp180) REVERT: G 21 MET cc_start: 0.5428 (mmm) cc_final: 0.5149 (mpt) REVERT: G 29 LYS cc_start: 0.7558 (mmtm) cc_final: 0.7335 (mptp) REVERT: N 1 GLN cc_start: 0.6177 (tp-100) cc_final: 0.5872 (mm-40) outliers start: 23 outliers final: 10 residues processed: 154 average time/residue: 1.6040 time to fit residues: 261.3541 Evaluate side-chains 148 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 336 HIS Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS A 213 GLN A 357 HIS A 390 GLN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10749 Z= 0.156 Angle : 0.553 13.645 14516 Z= 0.285 Chirality : 0.041 0.197 1594 Planarity : 0.003 0.038 1816 Dihedral : 10.394 98.558 1837 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.73 % Allowed : 13.92 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1254 helix: 2.24 (0.23), residues: 514 sheet: 0.10 (0.33), residues: 236 loop : 0.53 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR N 117 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0233 (ptm) cc_final: -0.0084 (tpp) REVERT: R 48 MET cc_start: 0.0332 (mmt) cc_final: -0.0228 (tmt) REVERT: R 169 ILE cc_start: 0.6507 (mt) cc_final: 0.6103 (mm) REVERT: R 174 ARG cc_start: 0.4798 (OUTLIER) cc_final: 0.4390 (mtm180) REVERT: R 195 SER cc_start: 0.7075 (m) cc_final: 0.6613 (p) REVERT: R 230 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6663 (ttm) REVERT: R 314 PHE cc_start: 0.6229 (m-80) cc_final: 0.5666 (t80) REVERT: A 16 GLU cc_start: 0.5389 (tp30) cc_final: 0.4624 (tp30) REVERT: A 17 LYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5250 (mtpt) REVERT: A 20 ARG cc_start: 0.6244 (mtm110) cc_final: 0.5917 (ttp-110) REVERT: A 28 LYS cc_start: 0.7082 (ttpp) cc_final: 0.6816 (ttpp) REVERT: A 265 ARG cc_start: 0.6774 (ptt-90) cc_final: 0.6168 (ppt90) REVERT: B 214 ARG cc_start: 0.6579 (mtm180) cc_final: 0.6375 (mtp180) REVERT: G 21 MET cc_start: 0.5414 (mmm) cc_final: 0.5144 (mpt) REVERT: G 29 LYS cc_start: 0.7609 (mmtm) cc_final: 0.7365 (mptp) REVERT: N 1 GLN cc_start: 0.6164 (tp-100) cc_final: 0.5858 (mm-40) outliers start: 19 outliers final: 10 residues processed: 151 average time/residue: 1.6507 time to fit residues: 263.7875 Evaluate side-chains 150 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 336 HIS Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 0.1980 chunk 76 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10749 Z= 0.164 Angle : 0.565 12.986 14516 Z= 0.291 Chirality : 0.042 0.202 1594 Planarity : 0.004 0.039 1816 Dihedral : 10.403 96.446 1837 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.36 % Allowed : 14.10 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1254 helix: 2.17 (0.23), residues: 514 sheet: 0.10 (0.33), residues: 236 loop : 0.51 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 234 HIS 0.005 0.001 HIS R 336 PHE 0.015 0.002 PHE A 212 TYR 0.013 0.001 TYR R 338 ARG 0.002 0.000 ARG A 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: 0.0198 (ptm) cc_final: -0.0106 (tpp) REVERT: R 48 MET cc_start: 0.0330 (mmt) cc_final: -0.0214 (tmt) REVERT: R 169 ILE cc_start: 0.6521 (mt) cc_final: 0.6094 (mm) REVERT: R 174 ARG cc_start: 0.4803 (OUTLIER) cc_final: 0.4393 (mtm180) REVERT: R 195 SER cc_start: 0.7080 (m) cc_final: 0.6612 (p) REVERT: R 230 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6681 (ttm) REVERT: R 314 PHE cc_start: 0.6229 (m-80) cc_final: 0.5667 (t80) REVERT: A 16 GLU cc_start: 0.5394 (tp30) cc_final: 0.4627 (tp30) REVERT: A 17 LYS cc_start: 0.5696 (OUTLIER) cc_final: 0.5245 (mtpt) REVERT: A 20 ARG cc_start: 0.6217 (mtm110) cc_final: 0.5889 (ttp-110) REVERT: A 28 LYS cc_start: 0.7080 (ttpp) cc_final: 0.6787 (ttpp) REVERT: A 265 ARG cc_start: 0.6775 (ptt-90) cc_final: 0.6161 (ppt90) REVERT: B 214 ARG cc_start: 0.6645 (mtm180) cc_final: 0.6419 (mtp180) REVERT: G 21 MET cc_start: 0.5411 (mmm) cc_final: 0.5138 (mpt) REVERT: G 29 LYS cc_start: 0.7614 (mmtm) cc_final: 0.7374 (mptp) REVERT: N 1 GLN cc_start: 0.6162 (tp-100) cc_final: 0.5852 (mm-40) outliers start: 15 outliers final: 10 residues processed: 145 average time/residue: 1.6578 time to fit residues: 254.7323 Evaluate side-chains 147 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN B 266 HIS B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.234221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.210812 restraints weight = 7007.278| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 0.54 r_work: 0.4122 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10749 Z= 0.158 Angle : 0.545 11.897 14516 Z= 0.283 Chirality : 0.041 0.200 1594 Planarity : 0.004 0.039 1816 Dihedral : 10.164 91.005 1837 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.55 % Allowed : 14.01 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1254 helix: 2.24 (0.23), residues: 514 sheet: 0.22 (0.33), residues: 231 loop : 0.49 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.004 0.001 HIS R 336 PHE 0.015 0.001 PHE A 212 TYR 0.009 0.001 TYR N 117 ARG 0.002 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4929.23 seconds wall clock time: 87 minutes 13.24 seconds (5233.24 seconds total)