Starting phenix.real_space_refine on Fri Dec 8 12:25:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/12_2023/7try_26103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/12_2023/7try_26103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/12_2023/7try_26103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/12_2023/7try_26103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/12_2023/7try_26103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/12_2023/7try_26103.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5281 2.51 5 N 1491 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 162": "NH1" <-> "NH2" Residue "P ARG 221": "NH1" <-> "NH2" Residue "P ARG 306": "NH1" <-> "NH2" Residue "P ARG 371": "NH1" <-> "NH2" Residue "P ARG 373": "NH1" <-> "NH2" Residue "U ARG 15": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 202": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8340 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2031 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 9, 'TRANS': 315} Chain breaks: 5 Unresolved non-hydrogen bonds: 746 Unresolved non-hydrogen angles: 967 Unresolved non-hydrogen dihedrals: 628 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 11, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 5, 'PHE:plan': 16, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 423 Chain: "U" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 233 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 1, 'TRANS': 37} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1642 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2385 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 141 Chain: "G" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 372 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1677 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 4.82, per 1000 atoms: 0.58 Number of scatterers: 8340 At special positions: 0 Unit cell: (105.545, 137.94, 145.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1529 8.00 N 1491 7.00 C 5281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS P 64 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS P 184 " - pdb=" SG CYS P 254 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2286 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 40.3% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'P' and resid 109 through 141 removed outlier: 3.790A pdb=" N TYR P 113 " --> pdb=" O TYR P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 169 Processing helix chain 'P' and resid 173 through 179 Processing helix chain 'P' and resid 181 through 215 Processing helix chain 'P' and resid 215 through 222 removed outlier: 3.843A pdb=" N GLU P 220 " --> pdb=" O THR P 216 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 233 removed outlier: 3.708A pdb=" N PHE P 227 " --> pdb=" O ARG P 223 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE P 229 " --> pdb=" O CYS P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 250 removed outlier: 3.957A pdb=" N ILE P 238 " --> pdb=" O ILE P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 298 Proline residue: P 271 - end of helix removed outlier: 3.505A pdb=" N LEU P 274 " --> pdb=" O GLY P 270 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 319 Proline residue: P 317 - end of helix Processing helix chain 'P' and resid 321 through 326 removed outlier: 4.002A pdb=" N PHE P 326 " --> pdb=" O THR P 322 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 361 removed outlier: 4.422A pdb=" N GLY P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE P 353 " --> pdb=" O SER P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 383 Processing helix chain 'U' and resid 5 through 7 No H-bonds generated for 'chain 'U' and resid 5 through 7' Processing helix chain 'U' and resid 8 through 40 Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 51 through 61 removed outlier: 3.955A pdb=" N ILE A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.865A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 221 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.131A pdb=" N ASP A 236 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 275 through 286 removed outlier: 3.819A pdb=" N LEU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.032A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 37 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.962A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.569A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 62 through 63 removed outlier: 3.631A pdb=" N TYR P 80 " --> pdb=" O ASN P 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 67 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.434A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 10.708A pdb=" N SER A 225 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 52 removed outlier: 7.031A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.839A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.070A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.548A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.010A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.730A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.150A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.790A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 7.032A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 146 through 148 removed outlier: 4.102A pdb=" N GLN H 231 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR H 238 " --> pdb=" O GLN H 231 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1377 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: 2.66 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2773 1.34 - 1.47: 2143 1.47 - 1.59: 3537 1.59 - 1.71: 0 1.71 - 1.83: 53 Bond restraints: 8506 Sorted by residual: bond pdb=" C PHE P 236 " pdb=" N PRO P 237 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.25e-02 6.40e+03 2.50e+00 bond pdb=" C ASP H 74 " pdb=" N PRO H 75 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.25e-02 6.40e+03 2.41e+00 bond pdb=" C ILE P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 1.336 1.353 -0.018 1.25e-02 6.40e+03 1.98e+00 bond pdb=" CB ASN B 237 " pdb=" CG ASN B 237 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" C ALA H 40 " pdb=" N PRO H 41 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.46e+00 ... (remaining 8501 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.72: 105 104.72 - 112.05: 4158 112.05 - 119.37: 2675 119.37 - 126.69: 4565 126.69 - 134.02: 136 Bond angle restraints: 11639 Sorted by residual: angle pdb=" N GLY P 270 " pdb=" CA GLY P 270 " pdb=" C GLY P 270 " ideal model delta sigma weight residual 112.34 119.59 -7.25 2.04e+00 2.40e-01 1.26e+01 angle pdb=" N ILE P 234 " pdb=" CA ILE P 234 " pdb=" C ILE P 234 " ideal model delta sigma weight residual 112.35 116.56 -4.21 1.20e+00 6.94e-01 1.23e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" N MET B 262 " pdb=" CA MET B 262 " pdb=" C MET B 262 " ideal model delta sigma weight residual 108.55 113.72 -5.17 1.62e+00 3.81e-01 1.02e+01 angle pdb=" C PHE P 327 " pdb=" N VAL P 328 " pdb=" CA VAL P 328 " ideal model delta sigma weight residual 121.70 127.14 -5.44 1.80e+00 3.09e-01 9.14e+00 ... (remaining 11634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.89: 4606 9.89 - 19.79: 291 19.79 - 29.68: 32 29.68 - 39.57: 16 39.57 - 49.47: 7 Dihedral angle restraints: 4952 sinusoidal: 1433 harmonic: 3519 Sorted by residual: dihedral pdb=" CA CYS P 254 " pdb=" C CYS P 254 " pdb=" N TRP P 255 " pdb=" CA TRP P 255 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE H 32 " pdb=" C PHE H 32 " pdb=" N GLY H 33 " pdb=" CA GLY H 33 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 961 0.045 - 0.089: 297 0.089 - 0.134: 89 0.134 - 0.179: 27 0.179 - 0.223: 5 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA ILE H 100 " pdb=" N ILE H 100 " pdb=" C ILE H 100 " pdb=" CB ILE H 100 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PHE P 236 " pdb=" N PHE P 236 " pdb=" C PHE P 236 " pdb=" CB PHE P 236 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CG LEU H 174 " pdb=" CB LEU H 174 " pdb=" CD1 LEU H 174 " pdb=" CD2 LEU H 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1376 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 276 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C LEU P 276 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU P 276 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU P 277 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 159 " -0.014 2.00e-02 2.50e+03 2.11e-02 7.76e+00 pdb=" CG PHE P 159 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE P 159 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE P 159 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE P 159 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE P 159 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE P 159 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 288 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C ARG P 288 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG P 288 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE P 289 " -0.016 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1680 2.79 - 3.32: 7543 3.32 - 3.84: 13538 3.84 - 4.37: 14606 4.37 - 4.90: 26214 Nonbonded interactions: 63581 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.261 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.321 2.440 nonbonded pdb=" NZ LYS A 215 " pdb=" OD1 ASN B 230 " model vdw 2.350 2.520 nonbonded pdb=" NH2 ARG P 376 " pdb=" O HIS B 311 " model vdw 2.358 2.520 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.362 2.440 ... (remaining 63576 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 2.980 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.740 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 0.047 8506 Z= 0.248 Angle : 0.803 10.254 11639 Z= 0.487 Chirality : 0.050 0.223 1379 Planarity : 0.006 0.042 1511 Dihedral : 7.340 42.297 2654 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.03 (0.23), residues: 1185 helix: 1.35 (0.22), residues: 420 sheet: 0.61 (0.29), residues: 270 loop : 0.29 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.014 0.003 HIS P 152 PHE 0.048 0.003 PHE P 159 TYR 0.019 0.002 TYR A 356 ARG 0.006 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2221 time to fit residues: 107.1378 Evaluate side-chains 195 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 124 HIS P 152 HIS P 170 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN B 32 GLN B 88 ASN B 91 HIS B 183 HIS ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN H 231 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8506 Z= 0.320 Angle : 0.642 9.351 11639 Z= 0.344 Chirality : 0.045 0.221 1379 Planarity : 0.005 0.056 1511 Dihedral : 4.376 28.793 1284 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 6.07 % Allowed : 16.27 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.91 (0.24), residues: 1185 helix: 2.58 (0.23), residues: 429 sheet: 0.88 (0.31), residues: 268 loop : 0.39 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 82 HIS 0.006 0.002 HIS H 35 PHE 0.021 0.002 PHE A 55 TYR 0.017 0.002 TYR P 305 ARG 0.007 0.001 ARG P 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 28 residues processed: 225 average time/residue: 0.1780 time to fit residues: 57.0566 Evaluate side-chains 202 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1094 time to fit residues: 6.2419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 124 HIS P 198 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8506 Z= 0.195 Angle : 0.556 8.063 11639 Z= 0.291 Chirality : 0.044 0.212 1379 Planarity : 0.003 0.040 1511 Dihedral : 4.022 22.511 1284 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.37 % Allowed : 19.38 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.08 (0.25), residues: 1185 helix: 2.83 (0.23), residues: 430 sheet: 0.90 (0.33), residues: 245 loop : 0.42 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP P 201 HIS 0.006 0.001 HIS B 54 PHE 0.015 0.002 PHE B 253 TYR 0.014 0.002 TYR A 192 ARG 0.004 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 208 average time/residue: 0.1813 time to fit residues: 53.9102 Evaluate side-chains 185 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0844 time to fit residues: 2.9477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 154 ASN A 237 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8506 Z= 0.400 Angle : 0.643 9.302 11639 Z= 0.344 Chirality : 0.046 0.236 1379 Planarity : 0.004 0.040 1511 Dihedral : 4.408 17.348 1284 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.99 % Allowed : 18.79 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1185 helix: 2.63 (0.23), residues: 427 sheet: 0.46 (0.31), residues: 263 loop : 0.21 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP P 232 HIS 0.007 0.001 HIS B 142 PHE 0.028 0.002 PHE H 212 TYR 0.015 0.002 TYR H 59 ARG 0.007 0.001 ARG U 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 199 average time/residue: 0.1693 time to fit residues: 49.6404 Evaluate side-chains 174 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1114 time to fit residues: 3.9465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8506 Z= 0.272 Angle : 0.600 9.044 11639 Z= 0.314 Chirality : 0.044 0.294 1379 Planarity : 0.004 0.040 1511 Dihedral : 4.256 21.232 1284 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.66 % Allowed : 22.19 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.61 (0.25), residues: 1185 helix: 2.69 (0.24), residues: 428 sheet: 0.32 (0.32), residues: 258 loop : 0.10 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 332 HIS 0.004 0.001 HIS B 54 PHE 0.022 0.002 PHE H 212 TYR 0.012 0.002 TYR H 190 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 192 average time/residue: 0.1708 time to fit residues: 48.7244 Evaluate side-chains 170 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0785 time to fit residues: 2.7732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 0.0970 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8506 Z= 0.450 Angle : 0.715 12.067 11639 Z= 0.375 Chirality : 0.047 0.358 1379 Planarity : 0.005 0.043 1511 Dihedral : 4.724 21.446 1284 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.29 % Allowed : 22.93 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.00 (0.25), residues: 1185 helix: 2.12 (0.24), residues: 438 sheet: 0.15 (0.32), residues: 254 loop : -0.34 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP P 232 HIS 0.006 0.002 HIS B 142 PHE 0.027 0.003 PHE B 292 TYR 0.014 0.002 TYR H 228 ARG 0.006 0.001 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 178 average time/residue: 0.1534 time to fit residues: 40.6272 Evaluate side-chains 166 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0867 time to fit residues: 3.8455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 149 ASN ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 198 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8506 Z= 0.179 Angle : 0.640 10.510 11639 Z= 0.320 Chirality : 0.044 0.226 1379 Planarity : 0.004 0.043 1511 Dihedral : 4.274 22.851 1284 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.18 % Allowed : 24.70 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.50 (0.25), residues: 1185 helix: 2.64 (0.24), residues: 431 sheet: 0.29 (0.32), residues: 262 loop : -0.04 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 111 HIS 0.004 0.001 HIS B 183 PHE 0.014 0.002 PHE H 177 TYR 0.021 0.002 TYR H 228 ARG 0.005 0.001 ARG P 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 189 average time/residue: 0.1612 time to fit residues: 45.4063 Evaluate side-chains 173 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0829 time to fit residues: 1.7243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 8506 Z= 0.526 Angle : 0.779 12.412 11639 Z= 0.408 Chirality : 0.048 0.274 1379 Planarity : 0.005 0.056 1511 Dihedral : 4.936 29.835 1284 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.37 % Allowed : 25.89 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.68 (0.25), residues: 1185 helix: 1.96 (0.25), residues: 436 sheet: -0.15 (0.31), residues: 270 loop : -0.53 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP P 232 HIS 0.008 0.002 HIS B 142 PHE 0.024 0.003 PHE P 138 TYR 0.022 0.003 TYR H 228 ARG 0.006 0.001 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 160 average time/residue: 0.1618 time to fit residues: 38.7098 Evaluate side-chains 152 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0856 time to fit residues: 2.6550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 149 ASN ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8506 Z= 0.213 Angle : 0.690 13.827 11639 Z= 0.341 Chirality : 0.045 0.327 1379 Planarity : 0.006 0.181 1511 Dihedral : 4.493 23.380 1284 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.89 % Allowed : 27.07 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.20 (0.25), residues: 1185 helix: 2.51 (0.24), residues: 430 sheet: -0.01 (0.32), residues: 270 loop : -0.24 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.018 0.002 PHE H 212 TYR 0.020 0.002 TYR H 228 ARG 0.017 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 173 average time/residue: 0.1674 time to fit residues: 43.2159 Evaluate side-chains 157 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0777 time to fit residues: 1.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 0.0010 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8506 Z= 0.214 Angle : 0.689 11.760 11639 Z= 0.339 Chirality : 0.045 0.280 1379 Planarity : 0.005 0.115 1511 Dihedral : 4.349 21.083 1284 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.89 % Allowed : 28.70 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.27 (0.26), residues: 1185 helix: 2.66 (0.24), residues: 431 sheet: -0.19 (0.31), residues: 277 loop : -0.15 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.026 0.002 PHE B 335 TYR 0.022 0.002 TYR H 228 ARG 0.013 0.001 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 172 average time/residue: 0.1568 time to fit residues: 40.5051 Evaluate side-chains 166 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 162 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0747 time to fit residues: 1.7892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.088323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072808 restraints weight = 30476.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.075197 restraints weight = 13990.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.076706 restraints weight = 8502.157| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8506 Z= 0.278 Angle : 0.701 13.019 11639 Z= 0.346 Chirality : 0.045 0.255 1379 Planarity : 0.005 0.089 1511 Dihedral : 4.370 21.337 1284 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.89 % Allowed : 28.99 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.27 (0.26), residues: 1185 helix: 2.72 (0.24), residues: 431 sheet: -0.28 (0.32), residues: 276 loop : -0.15 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.022 0.002 PHE B 335 TYR 0.026 0.002 TYR H 228 ARG 0.012 0.001 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.34 seconds wall clock time: 35 minutes 19.16 seconds (2119.16 seconds total)