Starting phenix.real_space_refine on Sat Jun 7 00:27:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7try_26103/06_2025/7try_26103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7try_26103/06_2025/7try_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/cci-nas-00/data/ceres_data/7try_26103/06_2025/7try_26103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7try_26103/06_2025/7try_26103.map" model { file = "/net/cci-nas-00/data/ceres_data/7try_26103/06_2025/7try_26103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7try_26103/06_2025/7try_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-5710/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: 5.73, per 1000 atoms: 0.69 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: 2.43 Conformation dependent library (CDL) restraints added in 1.3 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: 1.20 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: 2.70 Time building geometry restraints manager: 2.76 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: 0.470 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.810 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- 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 8510 Z= 0.213 Angle : 0.805 10.254 11647 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 Details of bonding type rmsd hydrogen bonds : bond 0.12922 ( 486) hydrogen bonds : angle 6.17424 ( 1377) SS BOND : bond 0.00488 ( 4) SS BOND : angle 2.19021 ( 8) covalent geometry : bond 0.00367 ( 8506) covalent geometry : angle 0.80274 (11639) *********************** 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 to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.908 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: 0.2193 time to fit residues: 105.4630 Evaluate side-chains 198 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.095053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079818 restraints weight = 30251.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.082363 restraints weight = 14157.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.083987 restraints weight = 8513.333| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 8510 Z= 0.144 Angle : 0.612 9.961 11647 Z= 0.324 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 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 486) hydrogen bonds : angle 4.62303 ( 1377) SS BOND : bond 0.01023 ( 4) SS BOND : angle 3.35443 ( 8) covalent geometry : bond 0.00312 ( 8506) covalent geometry : angle 0.60539 (11639) *********************** 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 to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.988 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: 0.8674 (mt) cc_final: 0.8103 (tp) REVERT: P 154 ASN cc_start: 0.9211 (m-40) cc_final: 0.8975 (m-40) REVERT: P 305 TYR cc_start: 0.5889 (m-10) cc_final: 0.4691 (t80) REVERT: P 312 THR cc_start: 0.9289 (m) cc_final: 0.8943 (t) REVERT: A 24 MET cc_start: 0.8080 (tmm) cc_final: 0.7721 (tmm) REVERT: A 274 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.7888 (p0) REVERT: A 312 MET cc_start: 0.7908 (tmm) cc_final: 0.7636 (tmm) REVERT: B 52 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7692 (ptp-110) REVERT: B 135 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8560 (t) REVERT: B 146 LEU cc_start: 0.8589 (tp) cc_final: 0.8164 (mp) REVERT: B 241 PHE cc_start: 0.8921 (p90) cc_final: 0.8325 (p90) REVERT: B 289 TYR cc_start: 0.8250 (m-80) cc_final: 0.7900 (m-80) REVERT: B 297 TRP cc_start: 0.7844 (m100) cc_final: 0.7585 (m100) REVERT: G 15 LEU cc_start: 0.9175 (mt) cc_final: 0.8953 (mt) outliers start: 28 outliers final: 18 residues processed: 223 average time/residue: 0.1708 time to fit residues: 54.1444 Evaluate side-chains 203 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 92 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.092841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.077230 restraints weight = 31132.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079821 restraints weight = 14137.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.081474 restraints weight = 8463.378| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8510 Z= 0.193 Angle : 0.584 7.734 11647 Z= 0.310 Chirality : 0.044 0.202 1379 Planarity : 0.004 0.041 1511 Dihedral : 4.088 19.058 1284 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.88 % Allowed : 17.60 % 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: 1.98 (0.24), residues: 1185 helix: 2.89 (0.23), residues: 423 sheet: 0.77 (0.32), residues: 250 loop : 0.31 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 201 HIS 0.010 0.001 HIS B 266 PHE 0.024 0.002 PHE A 55 TYR 0.015 0.002 TYR H 190 ARG 0.008 0.001 ARG U 27 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 486) hydrogen bonds : angle 4.47188 ( 1377) SS BOND : bond 0.00325 ( 4) SS BOND : angle 1.64434 ( 8) covalent geometry : bond 0.00415 ( 8506) covalent geometry : angle 0.58235 (11639) *********************** 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 233 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 1.003 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 154 ASN cc_start: 0.8937 (m-40) cc_final: 0.8589 (t0) REVERT: P 159 PHE cc_start: 0.8879 (m-10) cc_final: 0.8636 (m-10) REVERT: P 305 TYR cc_start: 0.6238 (m-10) cc_final: 0.4959 (t80) REVERT: P 312 THR cc_start: 0.9377 (m) cc_final: 0.9011 (t) REVERT: A 24 MET cc_start: 0.8000 (tmm) cc_final: 0.7619 (tmm) REVERT: A 189 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7768 (tp) REVERT: A 312 MET cc_start: 0.7812 (tmm) cc_final: 0.7449 (tmm) REVERT: B 135 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8785 (t) REVERT: B 138 GLU cc_start: 0.8152 (mp0) cc_final: 0.7919 (mp0) REVERT: B 297 TRP cc_start: 0.8165 (m100) cc_final: 0.7768 (m100) REVERT: G 11 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8533 (tp-100) REVERT: G 15 LEU cc_start: 0.9144 (mt) cc_final: 0.8478 (mt) REVERT: H 229 CYS cc_start: 0.5343 (p) cc_final: 0.5137 (p) outliers start: 33 outliers final: 23 residues processed: 225 average time/residue: 0.1932 time to fit residues: 60.5289 Evaluate side-chains 195 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 376 ARG Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 217 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 58 ILE Chi-restraints excluded: chain B residue 70 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 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain H residue 64 VAL 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: 4.9990 chunk 41 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 237 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.089523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.073720 restraints weight = 31273.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076233 restraints weight = 14397.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.077817 restraints weight = 8671.910| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8510 Z= 0.248 Angle : 0.608 6.989 11647 Z= 0.329 Chirality : 0.045 0.232 1379 Planarity : 0.004 0.045 1511 Dihedral : 4.300 21.199 1284 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.47 % Allowed : 19.97 % Favored : 74.56 % 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: 1.73 (0.25), residues: 1185 helix: 2.70 (0.23), residues: 429 sheet: 0.40 (0.32), residues: 247 loop : 0.25 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 232 HIS 0.004 0.001 HIS A 327 PHE 0.017 0.002 PHE H 177 TYR 0.015 0.002 TYR P 359 ARG 0.006 0.001 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 486) hydrogen bonds : angle 4.52386 ( 1377) SS BOND : bond 0.00471 ( 4) SS BOND : angle 1.77938 ( 8) covalent geometry : bond 0.00530 ( 8506) covalent geometry : angle 0.60643 (11639) *********************** 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 to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.006 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: P 159 PHE cc_start: 0.8949 (m-10) cc_final: 0.8721 (m-10) REVERT: P 312 THR cc_start: 0.9390 (m) cc_final: 0.9078 (t) REVERT: A 24 MET cc_start: 0.7979 (tmm) cc_final: 0.7556 (tmm) REVERT: A 312 MET cc_start: 0.7875 (tmm) cc_final: 0.7418 (tmm) REVERT: B 85 TYR cc_start: 0.8808 (m-10) cc_final: 0.8064 (m-10) REVERT: B 292 PHE cc_start: 0.8581 (m-10) cc_final: 0.8187 (m-80) REVERT: G 11 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8574 (tp-100) REVERT: G 15 LEU cc_start: 0.9186 (mt) cc_final: 0.8467 (mt) REVERT: G 18 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7497 (tm-30) REVERT: G 22 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7216 (mt-10) REVERT: H 111 TRP cc_start: 0.8411 (m-10) cc_final: 0.8164 (m-10) outliers start: 37 outliers final: 26 residues processed: 210 average time/residue: 0.1649 time to fit residues: 50.0506 Evaluate side-chains 192 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 U residue 5 LEU 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 319 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG 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 111 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** ** 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 = 0.3784 r_free = 0.3784 target = 0.089776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.074147 restraints weight = 30739.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.076570 restraints weight = 14357.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078139 restraints weight = 8763.608| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8510 Z= 0.173 Angle : 0.573 7.785 11647 Z= 0.300 Chirality : 0.044 0.223 1379 Planarity : 0.003 0.043 1511 Dihedral : 4.202 18.838 1284 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.59 % Allowed : 22.49 % Favored : 72.93 % 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: 1.84 (0.25), residues: 1185 helix: 2.93 (0.24), residues: 427 sheet: 0.39 (0.32), residues: 258 loop : 0.24 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 232 HIS 0.005 0.001 HIS B 54 PHE 0.011 0.002 PHE H 32 TYR 0.020 0.002 TYR B 289 ARG 0.004 0.000 ARG U 27 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 486) hydrogen bonds : angle 4.33535 ( 1377) SS BOND : bond 0.00409 ( 4) SS BOND : angle 2.20941 ( 8) covalent geometry : bond 0.00381 ( 8506) covalent geometry : angle 0.56997 (11639) *********************** 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 222 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.999 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: P 159 PHE cc_start: 0.8925 (m-10) cc_final: 0.8696 (m-10) REVERT: P 312 THR cc_start: 0.9367 (m) cc_final: 0.9082 (t) REVERT: A 312 MET cc_start: 0.7859 (tmm) cc_final: 0.7403 (tmm) REVERT: B 85 TYR cc_start: 0.8880 (m-10) cc_final: 0.8068 (m-10) REVERT: B 117 LEU cc_start: 0.8911 (mt) cc_final: 0.8308 (mp) REVERT: B 200 VAL cc_start: 0.9280 (t) cc_final: 0.9042 (t) REVERT: G 15 LEU cc_start: 0.9223 (mt) cc_final: 0.8937 (mt) REVERT: H 111 TRP cc_start: 0.8403 (m-10) cc_final: 0.8185 (m-10) outliers start: 31 outliers final: 21 residues processed: 215 average time/residue: 0.1746 time to fit residues: 53.4988 Evaluate side-chains 191 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 322 THR Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain A residue 206 VAL 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 79 LEU 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 225 HIS Chi-restraints excluded: chain B residue 234 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 7 optimal weight: 10.0000 chunk 61 optimal weight: 0.0470 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 1.2482 ------------------------------------------------------------------------------- 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 299 GLN A 352 ASN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.090876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.075359 restraints weight = 30408.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.077898 restraints weight = 13689.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.079506 restraints weight = 8173.101| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8510 Z= 0.126 Angle : 0.563 8.734 11647 Z= 0.291 Chirality : 0.043 0.200 1379 Planarity : 0.004 0.053 1511 Dihedral : 4.104 21.357 1284 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.44 % Allowed : 24.11 % 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: 1.91 (0.25), residues: 1185 helix: 2.94 (0.24), residues: 431 sheet: 0.41 (0.33), residues: 255 loop : 0.31 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 332 HIS 0.005 0.001 HIS B 54 PHE 0.011 0.001 PHE P 159 TYR 0.013 0.002 TYR B 124 ARG 0.015 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 486) hydrogen bonds : angle 4.17745 ( 1377) SS BOND : bond 0.00378 ( 4) SS BOND : angle 2.04623 ( 8) covalent geometry : bond 0.00283 ( 8506) covalent geometry : angle 0.56095 (11639) *********************** 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 219 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 159 PHE cc_start: 0.8864 (m-10) cc_final: 0.8653 (m-10) REVERT: P 312 THR cc_start: 0.9362 (m) cc_final: 0.9084 (t) REVERT: A 312 MET cc_start: 0.7820 (tmm) cc_final: 0.7373 (tmm) REVERT: B 61 MET cc_start: 0.8452 (ppp) cc_final: 0.8196 (ptm) REVERT: B 85 TYR cc_start: 0.8852 (m-10) cc_final: 0.8084 (m-10) REVERT: B 117 LEU cc_start: 0.8942 (mt) cc_final: 0.8548 (mt) REVERT: B 188 MET cc_start: 0.8123 (mmm) cc_final: 0.7663 (mmm) REVERT: B 200 VAL cc_start: 0.9249 (t) cc_final: 0.8993 (t) REVERT: G 11 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8587 (tp-100) REVERT: G 15 LEU cc_start: 0.9236 (mt) cc_final: 0.8593 (mt) REVERT: G 18 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7598 (tp40) REVERT: H 111 TRP cc_start: 0.8352 (m-10) cc_final: 0.7943 (m-10) outliers start: 30 outliers final: 21 residues processed: 208 average time/residue: 0.2072 time to fit residues: 62.7438 Evaluate side-chains 196 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 275 VAL 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 329 THR Chi-restraints excluded: chain B residue 70 LEU 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 192 LEU 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 64 VAL 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 17 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.081352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065249 restraints weight = 31801.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067406 restraints weight = 14560.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068795 restraints weight = 8916.218| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8510 Z= 0.316 Angle : 0.692 8.971 11647 Z= 0.369 Chirality : 0.046 0.212 1379 Planarity : 0.005 0.046 1511 Dihedral : 4.646 18.327 1284 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.03 % Allowed : 23.22 % 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: 1.30 (0.25), residues: 1185 helix: 2.49 (0.24), residues: 434 sheet: 0.06 (0.32), residues: 265 loop : -0.12 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP P 232 HIS 0.006 0.001 HIS B 54 PHE 0.018 0.003 PHE H 32 TYR 0.020 0.002 TYR B 124 ARG 0.012 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 486) hydrogen bonds : angle 4.68548 ( 1377) SS BOND : bond 0.00484 ( 4) SS BOND : angle 2.50868 ( 8) covalent geometry : bond 0.00672 ( 8506) covalent geometry : angle 0.68944 (11639) *********************** 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 202 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9373 (m) cc_final: 0.9151 (t) REVERT: P 383 LEU cc_start: 0.6722 (tp) cc_final: 0.6512 (tp) REVERT: A 14 GLU cc_start: 0.8892 (pm20) cc_final: 0.8631 (pm20) REVERT: A 20 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8987 (tm-30) REVERT: A 24 MET cc_start: 0.8274 (tmm) cc_final: 0.7810 (tmm) REVERT: A 312 MET cc_start: 0.8206 (tmm) cc_final: 0.7555 (tmm) REVERT: B 85 TYR cc_start: 0.9174 (m-10) cc_final: 0.8357 (m-10) REVERT: B 291 ASP cc_start: 0.8472 (m-30) cc_final: 0.7752 (m-30) REVERT: G 11 GLN cc_start: 0.9280 (tp-100) cc_final: 0.8875 (tp-100) REVERT: G 15 LEU cc_start: 0.9331 (mt) cc_final: 0.8879 (mt) REVERT: H 111 TRP cc_start: 0.8738 (m-10) cc_final: 0.8487 (m-10) outliers start: 34 outliers final: 23 residues processed: 189 average time/residue: 0.1835 time to fit residues: 49.9937 Evaluate side-chains 186 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 56 ILE 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 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE 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 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain G residue 51 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 29 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 0.0270 chunk 66 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.0030 overall best weight: 0.5050 ------------------------------------------------------------------------------- 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** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.085287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.069318 restraints weight = 31016.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.071664 restraints weight = 13972.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073176 restraints weight = 8356.635| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8510 Z= 0.118 Angle : 0.627 11.383 11647 Z= 0.313 Chirality : 0.044 0.197 1379 Planarity : 0.003 0.045 1511 Dihedral : 4.242 22.896 1284 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.40 % Allowed : 26.33 % Favored : 70.27 % 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: 1.72 (0.26), residues: 1185 helix: 2.89 (0.24), residues: 431 sheet: 0.01 (0.34), residues: 251 loop : 0.27 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 263 HIS 0.003 0.001 HIS B 311 PHE 0.014 0.002 PHE B 253 TYR 0.014 0.001 TYR B 124 ARG 0.007 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 486) hydrogen bonds : angle 4.19574 ( 1377) SS BOND : bond 0.00676 ( 4) SS BOND : angle 2.11681 ( 8) covalent geometry : bond 0.00260 ( 8506) covalent geometry : angle 0.62431 (11639) *********************** 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 215 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9278 (m) cc_final: 0.9053 (t) REVERT: A 20 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8932 (tm-30) REVERT: A 191 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 243 ASP cc_start: 0.7933 (p0) cc_final: 0.7392 (p0) REVERT: A 276 LYS cc_start: 0.9061 (pttt) cc_final: 0.8814 (ptpt) REVERT: A 312 MET cc_start: 0.8063 (tmm) cc_final: 0.7496 (tmm) REVERT: B 85 TYR cc_start: 0.9085 (m-10) cc_final: 0.8160 (m-10) REVERT: B 291 ASP cc_start: 0.8460 (m-30) cc_final: 0.7727 (m-30) REVERT: B 292 PHE cc_start: 0.8389 (m-80) cc_final: 0.8139 (m-80) REVERT: G 11 GLN cc_start: 0.9216 (tp-100) cc_final: 0.8813 (tp-100) REVERT: G 15 LEU cc_start: 0.9322 (mt) cc_final: 0.8771 (mt) REVERT: H 34 MET cc_start: 0.8890 (mmm) cc_final: 0.8671 (mmm) REVERT: H 111 TRP cc_start: 0.8638 (m-10) cc_final: 0.8161 (m-10) REVERT: H 188 LEU cc_start: 0.9043 (mt) cc_final: 0.8489 (pp) outliers start: 23 outliers final: 19 residues processed: 206 average time/residue: 0.1781 time to fit residues: 52.0237 Evaluate side-chains 190 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 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 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 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 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: 8.9990 chunk 74 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 47 optimal weight: 0.0020 chunk 93 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.086133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070574 restraints weight = 31125.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072890 restraints weight = 13891.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.074380 restraints weight = 8248.648| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8510 Z= 0.117 Angle : 0.620 11.444 11647 Z= 0.312 Chirality : 0.043 0.168 1379 Planarity : 0.004 0.045 1511 Dihedral : 4.150 23.360 1284 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.96 % Allowed : 26.78 % Favored : 70.27 % 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: 1.72 (0.25), residues: 1185 helix: 2.91 (0.24), residues: 430 sheet: 0.06 (0.34), residues: 249 loop : 0.22 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 263 HIS 0.002 0.001 HIS B 54 PHE 0.013 0.001 PHE A 255 TYR 0.014 0.001 TYR B 264 ARG 0.007 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 486) hydrogen bonds : angle 4.16870 ( 1377) SS BOND : bond 0.00712 ( 4) SS BOND : angle 2.19002 ( 8) covalent geometry : bond 0.00266 ( 8506) covalent geometry : angle 0.61765 (11639) *********************** 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 202 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9257 (m) cc_final: 0.9014 (t) REVERT: A 20 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8895 (tm-30) REVERT: A 276 LYS cc_start: 0.9075 (pttt) cc_final: 0.8845 (ptpt) REVERT: B 82 TRP cc_start: 0.9023 (m100) cc_final: 0.8458 (m-10) REVERT: B 85 TYR cc_start: 0.9080 (m-10) cc_final: 0.8178 (m-10) REVERT: B 291 ASP cc_start: 0.8415 (m-30) cc_final: 0.7705 (m-30) REVERT: B 292 PHE cc_start: 0.8350 (m-80) cc_final: 0.8077 (m-80) REVERT: G 11 GLN cc_start: 0.9215 (tp-100) cc_final: 0.8805 (tp-100) REVERT: G 15 LEU cc_start: 0.9305 (mt) cc_final: 0.8758 (mt) REVERT: G 18 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8708 (tm-30) REVERT: G 22 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7200 (mt-10) REVERT: H 34 MET cc_start: 0.8974 (mmm) cc_final: 0.8729 (mmm) REVERT: H 111 TRP cc_start: 0.8638 (m-10) cc_final: 0.8186 (m-10) REVERT: H 188 LEU cc_start: 0.9033 (mt) cc_final: 0.8466 (pp) outliers start: 20 outliers final: 17 residues processed: 194 average time/residue: 0.2089 time to fit residues: 59.8929 Evaluate side-chains 185 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 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 79 LEU Chi-restraints excluded: chain B residue 135 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 91 HIS ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.089358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.073717 restraints weight = 30769.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076145 restraints weight = 13986.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.077703 restraints weight = 8449.763| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8510 Z= 0.170 Angle : 0.632 12.287 11647 Z= 0.322 Chirality : 0.044 0.165 1379 Planarity : 0.004 0.044 1511 Dihedral : 4.156 19.101 1284 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.11 % Allowed : 27.07 % Favored : 69.82 % 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: 1.73 (0.26), residues: 1185 helix: 2.91 (0.24), residues: 431 sheet: 0.18 (0.33), residues: 267 loop : 0.16 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 232 HIS 0.007 0.001 HIS B 91 PHE 0.017 0.002 PHE B 335 TYR 0.016 0.002 TYR B 124 ARG 0.008 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 486) hydrogen bonds : angle 4.18532 ( 1377) SS BOND : bond 0.00542 ( 4) SS BOND : angle 2.41096 ( 8) covalent geometry : bond 0.00380 ( 8506) covalent geometry : angle 0.62944 (11639) ********************** 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 188 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 312 THR cc_start: 0.9297 (m) cc_final: 0.9045 (t) REVERT: A 276 LYS cc_start: 0.8962 (pttt) cc_final: 0.8750 (ptpt) REVERT: A 312 MET cc_start: 0.7791 (tmm) cc_final: 0.7326 (tmm) REVERT: B 82 TRP cc_start: 0.8965 (m100) cc_final: 0.8541 (m-10) REVERT: B 85 TYR cc_start: 0.8872 (m-10) cc_final: 0.8248 (m-10) REVERT: B 291 ASP cc_start: 0.8256 (m-30) cc_final: 0.7735 (m-30) REVERT: G 11 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8697 (tp-100) REVERT: G 15 LEU cc_start: 0.9253 (mt) cc_final: 0.8604 (mt) REVERT: G 18 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8630 (tm-30) REVERT: G 22 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7214 (mt-10) REVERT: H 34 MET cc_start: 0.8760 (mmm) cc_final: 0.8253 (mmm) REVERT: H 111 TRP cc_start: 0.8401 (m-10) cc_final: 0.8133 (m-10) outliers start: 21 outliers final: 17 residues processed: 180 average time/residue: 0.1538 time to fit residues: 40.6713 Evaluate side-chains 185 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 322 THR Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain U residue 7 ILE Chi-restraints excluded: chain A residue 56 ILE 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 79 LEU Chi-restraints excluded: chain B residue 135 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.0980 chunk 7 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.089595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.073750 restraints weight = 30947.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076218 restraints weight = 14022.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.077807 restraints weight = 8450.002| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8510 Z= 0.154 Angle : 0.629 12.240 11647 Z= 0.319 Chirality : 0.043 0.168 1379 Planarity : 0.003 0.042 1511 Dihedral : 4.106 18.952 1284 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.66 % Allowed : 27.81 % Favored : 69.53 % 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: 1.72 (0.26), residues: 1185 helix: 2.94 (0.24), residues: 429 sheet: 0.07 (0.33), residues: 259 loop : 0.19 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 232 HIS 0.003 0.001 HIS B 54 PHE 0.015 0.002 PHE B 335 TYR 0.015 0.002 TYR B 124 ARG 0.007 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 486) hydrogen bonds : angle 4.16093 ( 1377) SS BOND : bond 0.00456 ( 4) SS BOND : angle 2.27245 ( 8) covalent geometry : bond 0.00349 ( 8506) covalent geometry : angle 0.62648 (11639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3646.36 seconds wall clock time: 65 minutes 11.79 seconds (3911.79 seconds total)