Starting phenix.real_space_refine on Tue Sep 24 15:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/09_2024/7try_26103.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/09_2024/7try_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_26103/09_2024/7try_26103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/09_2024/7try_26103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/09_2024/7try_26103.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7try_26103/09_2024/7try_26103.cif" } 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. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.39, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 2.24 Conformation dependent library (CDL) restraints added in 1.2 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: 1.25 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: 2.65 Time building geometry restraints manager: 2.62 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: 0.00 - 2.05: 11286 2.05 - 4.10: 310 4.10 - 6.15: 31 6.15 - 8.20: 11 8.20 - 10.25: 1 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 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.321 3.040 nonbonded pdb=" NZ LYS A 215 " pdb=" OD1 ASN B 230 " model vdw 2.350 3.120 nonbonded pdb=" NH2 ARG P 376 " pdb=" O HIS B 311 " model vdw 2.358 3.120 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.362 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.700 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.780 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- 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 : 0.923 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: P 305 TYR cc_start: 0.5770 (m-10) cc_final: 0.4705 (t80) REVERT: P 312 THR cc_start: 0.9161 (m) cc_final: 0.8859 (t) REVERT: B 52 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7468 (ptp-110) REVERT: B 146 LEU cc_start: 0.8681 (tp) cc_final: 0.8169 (mp) REVERT: B 188 MET cc_start: 0.7922 (mmm) cc_final: 0.7550 (mmm) REVERT: B 241 PHE cc_start: 0.8381 (p90) cc_final: 0.8053 (p90) REVERT: G 22 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7046 (mt-10) REVERT: H 81 LEU cc_start: 0.8327 (tp) cc_final: 0.8060 (tp) REVERT: H 174 LEU cc_start: 0.8449 (tp) cc_final: 0.7563 (tp) REVERT: H 178 LEU cc_start: 0.8722 (tp) cc_final: 0.8407 (tt) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2247 time to fit residues: 107.9639 Evaluate side-chains 198 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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: 7.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 68 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 352 ASN B 32 GLN B 91 HIS B 183 HIS H 142 GLN H 231 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8506 Z= 0.207 Angle : 0.605 9.961 11639 Z= 0.322 Chirality : 0.044 0.203 1379 Planarity : 0.004 0.052 1511 Dihedral : 4.232 30.473 1284 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.14 % Allowed : 16.72 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.86 (0.24), residues: 1185 helix: 2.66 (0.23), residues: 426 sheet: 0.77 (0.31), residues: 259 loop : 0.30 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 201 HIS 0.005 0.001 HIS B 183 PHE 0.021 0.002 PHE A 55 TYR 0.016 0.002 TYR B 289 ARG 0.007 0.001 ARG A 306 *********************** 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 231 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.002 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: P 151 ILE cc_start: 0.8676 (mt) cc_final: 0.8125 (tp) REVERT: P 305 TYR cc_start: 0.5891 (m-10) cc_final: 0.4677 (t80) REVERT: P 312 THR cc_start: 0.9298 (m) cc_final: 0.8950 (t) REVERT: A 24 MET cc_start: 0.7957 (tmm) cc_final: 0.7624 (tmm) REVERT: A 274 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7833 (p0) REVERT: A 312 MET cc_start: 0.7791 (tmm) cc_final: 0.7536 (tmm) REVERT: B 135 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8480 (t) REVERT: B 146 LEU cc_start: 0.8546 (tp) cc_final: 0.8219 (mp) REVERT: B 241 PHE cc_start: 0.8800 (p90) cc_final: 0.8227 (p90) REVERT: B 289 TYR cc_start: 0.8189 (m-80) cc_final: 0.7899 (m-80) REVERT: B 297 TRP cc_start: 0.7800 (m100) cc_final: 0.7587 (m100) REVERT: G 15 LEU cc_start: 0.9151 (mt) cc_final: 0.8921 (mt) outliers start: 28 outliers final: 18 residues processed: 223 average time/residue: 0.1769 time to fit residues: 55.7966 Evaluate side-chains 202 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 286 ILE Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 376 ARG Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8506 Z= 0.205 Angle : 0.556 8.097 11639 Z= 0.294 Chirality : 0.043 0.200 1379 Planarity : 0.004 0.041 1511 Dihedral : 3.951 23.056 1284 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.29 % Allowed : 18.20 % Favored : 77.51 % 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: 2.05 (0.24), residues: 1185 helix: 2.98 (0.23), residues: 423 sheet: 0.71 (0.31), residues: 264 loop : 0.36 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP P 201 HIS 0.005 0.001 HIS B 54 PHE 0.027 0.001 PHE A 55 TYR 0.013 0.002 TYR H 190 ARG 0.009 0.001 ARG U 27 *********************** 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 226 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.063 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: P 151 ILE cc_start: 0.8755 (mt) cc_final: 0.8475 (tp) REVERT: P 159 PHE cc_start: 0.8866 (m-10) cc_final: 0.8585 (m-10) REVERT: P 201 TRP cc_start: 0.7031 (m100) cc_final: 0.6404 (m100) REVERT: P 305 TYR cc_start: 0.5909 (m-10) cc_final: 0.4778 (t80) REVERT: P 312 THR cc_start: 0.9330 (m) cc_final: 0.8991 (t) REVERT: A 24 MET cc_start: 0.8006 (tmm) cc_final: 0.7656 (tmm) REVERT: A 41 LYS cc_start: 0.7677 (mppt) cc_final: 0.7396 (mppt) REVERT: A 189 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7522 (tp) REVERT: A 215 LYS cc_start: 0.9264 (mmmm) cc_final: 0.9017 (mmmm) REVERT: A 266 ASN cc_start: 0.7951 (t0) cc_final: 0.7677 (t0) REVERT: A 312 MET cc_start: 0.7800 (tmm) cc_final: 0.7473 (tmm) REVERT: B 82 TRP cc_start: 0.8903 (m100) cc_final: 0.8566 (m100) REVERT: B 135 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8615 (t) REVERT: B 297 TRP cc_start: 0.7967 (m100) cc_final: 0.7747 (m100) REVERT: G 11 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8541 (tp-100) REVERT: G 15 LEU cc_start: 0.9127 (mt) cc_final: 0.8438 (mt) REVERT: G 22 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6910 (mt-10) REVERT: G 57 SER cc_start: 0.8912 (p) cc_final: 0.8692 (t) REVERT: H 229 CYS cc_start: 0.5208 (p) cc_final: 0.4885 (p) outliers start: 29 outliers final: 18 residues processed: 217 average time/residue: 0.1760 time to fit residues: 54.1216 Evaluate side-chains 195 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 376 ARG Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 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: 0.7862 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8506 Z= 0.366 Angle : 0.616 7.555 11639 Z= 0.335 Chirality : 0.046 0.246 1379 Planarity : 0.004 0.043 1511 Dihedral : 4.268 21.095 1284 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.47 % Allowed : 18.93 % Favored : 75.59 % 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: 1.82 (0.25), residues: 1185 helix: 2.75 (0.23), residues: 426 sheet: 0.56 (0.32), residues: 256 loop : 0.27 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP P 201 HIS 0.004 0.001 HIS B 54 PHE 0.016 0.002 PHE H 177 TYR 0.016 0.002 TYR P 359 ARG 0.005 0.001 ARG A 306 *********************** 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 222 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 201 TRP cc_start: 0.7272 (m100) cc_final: 0.6339 (m100) REVERT: P 312 THR cc_start: 0.9381 (m) cc_final: 0.9044 (t) REVERT: A 24 MET cc_start: 0.8059 (tmm) cc_final: 0.7677 (tmm) REVERT: A 41 LYS cc_start: 0.7813 (mppt) cc_final: 0.7564 (mppt) REVERT: A 312 MET cc_start: 0.7944 (tmm) cc_final: 0.7488 (tmm) REVERT: B 82 TRP cc_start: 0.9046 (m100) cc_final: 0.8829 (m100) REVERT: B 85 TYR cc_start: 0.8893 (m-10) cc_final: 0.8120 (m-10) REVERT: B 292 PHE cc_start: 0.8680 (m-10) cc_final: 0.8134 (m-10) REVERT: G 15 LEU cc_start: 0.9200 (mt) cc_final: 0.8927 (mt) outliers start: 37 outliers final: 25 residues processed: 210 average time/residue: 0.1793 time to fit residues: 53.1973 Evaluate side-chains 187 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain P residue 322 THR Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 376 ARG Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** A 237 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: 0.7885 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8506 Z= 0.326 Angle : 0.612 8.040 11639 Z= 0.323 Chirality : 0.045 0.221 1379 Planarity : 0.004 0.044 1511 Dihedral : 4.316 20.116 1284 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.18 % Allowed : 21.01 % Favored : 73.82 % 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: 1.69 (0.25), residues: 1185 helix: 2.74 (0.24), residues: 425 sheet: 0.33 (0.32), residues: 260 loop : 0.20 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP P 201 HIS 0.007 0.001 HIS B 91 PHE 0.014 0.002 PHE H 32 TYR 0.016 0.002 TYR B 289 ARG 0.005 0.001 ARG U 27 *********************** 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 220 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9362 (m) cc_final: 0.9092 (t) REVERT: P 383 LEU cc_start: 0.6837 (tp) cc_final: 0.6630 (tp) REVERT: A 41 LYS cc_start: 0.7973 (mppt) cc_final: 0.7653 (mppt) REVERT: A 189 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7820 (tp) REVERT: A 312 MET cc_start: 0.7945 (tmm) cc_final: 0.7460 (tmm) REVERT: B 85 TYR cc_start: 0.8973 (m-10) cc_final: 0.8194 (m-10) REVERT: G 11 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8714 (tp-100) REVERT: G 15 LEU cc_start: 0.9255 (mt) cc_final: 0.8703 (mt) REVERT: G 18 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7234 (tm-30) REVERT: G 22 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7295 (mm-30) REVERT: H 111 TRP cc_start: 0.8386 (m-10) cc_final: 0.8173 (m-10) outliers start: 35 outliers final: 22 residues processed: 208 average time/residue: 0.1813 time to fit residues: 53.3091 Evaluate side-chains 187 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain P residue 322 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 0.2980 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** 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: 0.7891 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8506 Z= 0.298 Angle : 0.602 8.535 11639 Z= 0.314 Chirality : 0.044 0.202 1379 Planarity : 0.005 0.151 1511 Dihedral : 4.366 19.668 1284 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.03 % Allowed : 21.75 % Favored : 73.22 % 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: 1.67 (0.25), residues: 1185 helix: 2.75 (0.24), residues: 427 sheet: 0.43 (0.33), residues: 250 loop : 0.10 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 232 HIS 0.005 0.001 HIS B 54 PHE 0.013 0.002 PHE H 32 TYR 0.016 0.002 TYR B 124 ARG 0.004 0.001 ARG B 49 *********************** 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 210 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9369 (m) cc_final: 0.9118 (t) REVERT: A 24 MET cc_start: 0.8032 (tmm) cc_final: 0.7567 (tmm) REVERT: A 41 LYS cc_start: 0.7980 (mppt) cc_final: 0.7647 (mppt) REVERT: A 312 MET cc_start: 0.7912 (tmm) cc_final: 0.7433 (tmm) REVERT: B 85 TYR cc_start: 0.9000 (m-10) cc_final: 0.8248 (m-10) REVERT: G 11 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8720 (tp-100) REVERT: G 15 LEU cc_start: 0.9290 (mt) cc_final: 0.8641 (mt) REVERT: H 111 TRP cc_start: 0.8506 (m-10) cc_final: 0.7992 (m-10) outliers start: 34 outliers final: 25 residues processed: 200 average time/residue: 0.1839 time to fit residues: 51.7988 Evaluate side-chains 193 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain P residue 322 THR Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 chunk 71 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 149 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8506 Z= 0.181 Angle : 0.583 9.828 11639 Z= 0.297 Chirality : 0.044 0.236 1379 Planarity : 0.003 0.045 1511 Dihedral : 4.138 21.458 1284 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.55 % Allowed : 22.78 % Favored : 73.67 % 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: 1.86 (0.25), residues: 1185 helix: 2.90 (0.24), residues: 431 sheet: 0.42 (0.33), residues: 261 loop : 0.25 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE A 55 TYR 0.014 0.002 TYR B 124 ARG 0.004 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 215 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9345 (m) cc_final: 0.9113 (t) REVERT: A 41 LYS cc_start: 0.7912 (mppt) cc_final: 0.7638 (mppt) REVERT: A 312 MET cc_start: 0.7850 (tmm) cc_final: 0.7379 (tmm) REVERT: B 85 TYR cc_start: 0.8921 (m-10) cc_final: 0.8142 (m-10) REVERT: B 188 MET cc_start: 0.8227 (mmm) cc_final: 0.7695 (mmm) REVERT: G 11 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8687 (tp-100) REVERT: G 15 LEU cc_start: 0.9265 (mt) cc_final: 0.8643 (mt) REVERT: G 19 LEU cc_start: 0.9378 (mm) cc_final: 0.9176 (mm) REVERT: H 111 TRP cc_start: 0.8435 (m-10) cc_final: 0.8138 (m-10) outliers start: 24 outliers final: 19 residues processed: 205 average time/residue: 0.1574 time to fit residues: 47.3855 Evaluate side-chains 190 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 149 ASN Chi-restraints excluded: chain P residue 322 THR Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 149 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** 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: 0.7912 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8506 Z= 0.356 Angle : 0.645 11.230 11639 Z= 0.336 Chirality : 0.046 0.246 1379 Planarity : 0.004 0.045 1511 Dihedral : 4.324 18.444 1284 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.29 % Allowed : 24.26 % Favored : 71.45 % 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: 1.59 (0.25), residues: 1185 helix: 2.74 (0.24), residues: 430 sheet: 0.37 (0.33), residues: 253 loop : -0.02 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 82 HIS 0.004 0.001 HIS P 152 PHE 0.014 0.002 PHE H 32 TYR 0.018 0.002 TYR B 264 ARG 0.008 0.001 ARG H 202 *********************** 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 196 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9332 (m) cc_final: 0.9106 (t) REVERT: A 41 LYS cc_start: 0.8084 (mppt) cc_final: 0.7750 (mppt) REVERT: A 191 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 312 MET cc_start: 0.7978 (tmm) cc_final: 0.7483 (tmm) REVERT: B 85 TYR cc_start: 0.8982 (m-10) cc_final: 0.8236 (m-10) REVERT: G 11 GLN cc_start: 0.9135 (tp-100) cc_final: 0.8760 (tp-100) REVERT: G 15 LEU cc_start: 0.9285 (mt) cc_final: 0.8708 (mt) REVERT: G 18 GLN cc_start: 0.8697 (mp10) cc_final: 0.8156 (mm-40) REVERT: H 111 TRP cc_start: 0.8517 (m-10) cc_final: 0.8067 (m-10) outliers start: 29 outliers final: 23 residues processed: 183 average time/residue: 0.1586 time to fit residues: 42.5601 Evaluate side-chains 183 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 322 THR Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 149 ASN ** A 303 GLN ** 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: 0.7846 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8506 Z= 0.194 Angle : 0.636 12.751 11639 Z= 0.317 Chirality : 0.045 0.325 1379 Planarity : 0.004 0.044 1511 Dihedral : 4.161 21.334 1284 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.40 % Allowed : 25.59 % Favored : 71.01 % 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: 1.78 (0.26), residues: 1185 helix: 2.89 (0.24), residues: 431 sheet: 0.39 (0.33), residues: 261 loop : 0.13 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.002 PHE B 335 TYR 0.017 0.001 TYR A 192 ARG 0.008 0.001 ARG H 202 *********************** 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 206 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9258 (m) cc_final: 0.9034 (t) REVERT: A 41 LYS cc_start: 0.8014 (mppt) cc_final: 0.7738 (mppt) REVERT: B 85 TYR cc_start: 0.8928 (m-10) cc_final: 0.8157 (m-10) REVERT: B 91 HIS cc_start: 0.8158 (m90) cc_final: 0.7905 (m90) REVERT: B 291 ASP cc_start: 0.8515 (m-30) cc_final: 0.7935 (m-30) REVERT: G 11 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8807 (tp-100) REVERT: G 15 LEU cc_start: 0.9281 (mt) cc_final: 0.8682 (mt) REVERT: H 111 TRP cc_start: 0.8422 (m-10) cc_final: 0.8143 (m-10) REVERT: H 216 ILE cc_start: 0.8827 (mm) cc_final: 0.8415 (tp) outliers start: 23 outliers final: 21 residues processed: 196 average time/residue: 0.1705 time to fit residues: 48.5565 Evaluate side-chains 196 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 149 ASN Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 322 THR Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 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: 0.7928 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8506 Z= 0.373 Angle : 0.688 12.258 11639 Z= 0.354 Chirality : 0.047 0.282 1379 Planarity : 0.005 0.066 1511 Dihedral : 4.413 19.645 1284 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.70 % Allowed : 24.41 % Favored : 71.89 % 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: 1.53 (0.26), residues: 1185 helix: 2.72 (0.25), residues: 430 sheet: 0.08 (0.32), residues: 271 loop : 0.07 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP B 82 HIS 0.005 0.001 HIS P 152 PHE 0.026 0.002 PHE B 335 TYR 0.017 0.002 TYR A 192 ARG 0.008 0.001 ARG H 202 ********************** 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 195 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9298 (m) cc_final: 0.9075 (t) REVERT: A 24 MET cc_start: 0.8001 (tmm) cc_final: 0.7593 (tmm) REVERT: A 41 LYS cc_start: 0.8178 (mppt) cc_final: 0.7842 (mppt) REVERT: A 312 MET cc_start: 0.7870 (tmm) cc_final: 0.7406 (tmm) REVERT: B 85 TYR cc_start: 0.9031 (m-10) cc_final: 0.8307 (m-10) REVERT: B 91 HIS cc_start: 0.8354 (m90) cc_final: 0.8042 (m90) REVERT: G 11 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8793 (tp-100) REVERT: G 15 LEU cc_start: 0.9315 (mt) cc_final: 0.8731 (mt) REVERT: H 20 LEU cc_start: 0.8639 (mt) cc_final: 0.8432 (mm) REVERT: H 111 TRP cc_start: 0.8513 (m-10) cc_final: 0.8208 (m-10) REVERT: H 216 ILE cc_start: 0.8854 (mm) cc_final: 0.8478 (tp) outliers start: 25 outliers final: 23 residues processed: 185 average time/residue: 0.1715 time to fit residues: 45.3765 Evaluate side-chains 187 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 124 HIS Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 322 THR Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 0.0060 chunk 96 optimal weight: 0.0570 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.0270 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 149 ASN ** 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 = 0.3727 r_free = 0.3727 target = 0.087367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.071454 restraints weight = 30391.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073789 restraints weight = 14163.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.075284 restraints weight = 8692.983| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 8506 Z= 0.344 Angle : 0.988 59.200 11639 Z= 0.566 Chirality : 0.046 0.278 1379 Planarity : 0.004 0.061 1511 Dihedral : 4.419 19.523 1284 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.85 % Allowed : 25.74 % Favored : 70.41 % Cbeta Deviations : 0.09 % 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: 1.55 (0.25), residues: 1185 helix: 2.74 (0.25), residues: 430 sheet: 0.16 (0.33), residues: 256 loop : 0.03 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP B 82 HIS 0.005 0.001 HIS P 152 PHE 0.021 0.002 PHE B 335 TYR 0.013 0.002 TYR A 192 ARG 0.007 0.001 ARG H 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.61 seconds wall clock time: 37 minutes 12.10 seconds (2232.10 seconds total)