Starting phenix.real_space_refine on Sun Dec 29 20:13:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mjz_9135/12_2024/6mjz_9135.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mjz_9135/12_2024/6mjz_9135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mjz_9135/12_2024/6mjz_9135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mjz_9135/12_2024/6mjz_9135.map" model { file = "/net/cci-nas-00/data/ceres_data/6mjz_9135/12_2024/6mjz_9135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mjz_9135/12_2024/6mjz_9135.cif" } resolution = 4.3 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= 0.007 sd= 0.110 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 59 5.16 5 C 7228 2.51 5 N 1914 2.21 5 O 2235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3291 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3162 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3218 Classifications: {'peptide': 415} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 397} Chain breaks: 1 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 99} Time building chain proxies: 7.41, per 1000 atoms: 0.65 Number of scatterers: 11436 At special positions: 0 Unit cell: (101.2, 101.2, 158.4, 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 59 16.00 O 2235 8.00 N 1914 7.00 C 7228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.53 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.52 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 230 " distance=2.18 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.36 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.25 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.29 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.53 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.35 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 168 " distance=2.34 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 230 " distance=2.27 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.52 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.15 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.33 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.25 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.84 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.30 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 230 " distance=2.57 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.43 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.10 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.40 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.29 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.56 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: 2.54 Conformation dependent library (CDL) restraints added in 1.6 seconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 23 sheets defined 31.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.546A pdb=" N HIS A 27 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.516A pdb=" N ASP A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 124 through 139 removed outlier: 3.508A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.297A pdb=" N ARG A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 4.699A pdb=" N LYS A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL A 184 " --> pdb=" O ASN A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 191 through 212 removed outlier: 4.041A pdb=" N ALA A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 removed outlier: 4.218A pdb=" N TYR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.303A pdb=" N THR A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.513A pdb=" N ILE A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.951A pdb=" N ARG B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 90 removed outlier: 4.018A pdb=" N LYS B 87 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 89 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 153 removed outlier: 4.551A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.489A pdb=" N VAL B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix Processing helix chain 'B' and resid 191 through 214 removed outlier: 4.118A pdb=" N ALA B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 removed outlier: 3.894A pdb=" N ILE B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 4.510A pdb=" N GLU B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.796A pdb=" N THR B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 removed outlier: 4.160A pdb=" N CYS B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.601A pdb=" N GLN B 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.854A pdb=" N ILE B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 removed outlier: 4.356A pdb=" N HIS C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.889A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR C 71 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 137 removed outlier: 4.409A pdb=" N LEU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 4.043A pdb=" N LYS C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 removed outlier: 4.769A pdb=" N VAL C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Proline residue: C 185 - end of helix Processing helix chain 'C' and resid 191 through 214 removed outlier: 4.140A pdb=" N CYS C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.081A pdb=" N THR C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 358 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 473 Processing helix chain 'H' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 285 through 287 removed outlier: 4.507A pdb=" N THR A 286 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 40 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.678A pdb=" N VAL A 170 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 172 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 52 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.975A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.615A pdb=" N GLY A 324 " --> pdb=" O MET A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 removed outlier: 4.030A pdb=" N TRP A 308 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 379 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.533A pdb=" N ASP B 297 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N LEU B 289 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N ILE B 40 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR B 291 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET B 38 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.533A pdb=" N ASP B 297 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 172 through 173 removed outlier: 4.165A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.555A pdb=" N ALA B 385 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 410 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.589A pdb=" N ASP C 297 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.596A pdb=" N THR C 286 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 40 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY C 37 " --> pdb=" O TYR C 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.506A pdb=" N ASP C 268 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN C 279 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 266 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 300 through 303 Processing sheet with id=AB7, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=AB8, first strand: chain 'C' and resid 383 through 385 removed outlier: 3.522A pdb=" N VAL C 383 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 412 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA C 385 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 410 " --> pdb=" O ALA C 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.230A pdb=" N SER H 84 " --> pdb=" O GLU H 16 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU H 16 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.824A pdb=" N LYS H 58 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER H 35 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE H 37 " --> pdb=" O PHE H 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 12 through 14 removed outlier: 5.799A pdb=" N LEU L 13 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.590A pdb=" N THR L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.655A pdb=" N THR L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 51 " --> pdb=" O THR L 55 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N SER L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN L 39 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3727 1.34 - 1.47: 2671 1.47 - 1.60: 5148 1.60 - 1.73: 0 1.73 - 1.86: 72 Bond restraints: 11618 Sorted by residual: bond pdb=" CG1 ILE B 128 " pdb=" CD1 ILE B 128 " ideal model delta sigma weight residual 1.513 1.419 0.094 3.90e-02 6.57e+02 5.86e+00 bond pdb=" CG ARG B 365 " pdb=" CD ARG B 365 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" N ILE L 98 " pdb=" CA ILE L 98 " ideal model delta sigma weight residual 1.474 1.448 0.027 1.57e-02 4.06e+03 2.91e+00 bond pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.77e+00 bond pdb=" CB PRO A 185 " pdb=" CG PRO A 185 " ideal model delta sigma weight residual 1.492 1.410 0.082 5.00e-02 4.00e+02 2.72e+00 ... (remaining 11613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 14808 1.89 - 3.78: 789 3.78 - 5.67: 137 5.67 - 7.56: 26 7.56 - 9.45: 9 Bond angle restraints: 15769 Sorted by residual: angle pdb=" C LYS C 138 " pdb=" N GLN C 139 " pdb=" CA GLN C 139 " ideal model delta sigma weight residual 120.44 129.89 -9.45 1.30e+00 5.92e-01 5.28e+01 angle pdb=" CA TYR C 71 " pdb=" CB TYR C 71 " pdb=" CG TYR C 71 " ideal model delta sigma weight residual 113.90 122.74 -8.84 1.80e+00 3.09e-01 2.41e+01 angle pdb=" N ASN C 217 " pdb=" CA ASN C 217 " pdb=" C ASN C 217 " ideal model delta sigma weight residual 110.97 116.01 -5.04 1.09e+00 8.42e-01 2.14e+01 angle pdb=" N ASN C 217 " pdb=" CA ASN C 217 " pdb=" CB ASN C 217 " ideal model delta sigma weight residual 109.91 116.60 -6.69 1.46e+00 4.69e-01 2.10e+01 angle pdb=" C GLY C 225 " pdb=" N ILE C 226 " pdb=" CA ILE C 226 " ideal model delta sigma weight residual 121.97 129.57 -7.60 1.80e+00 3.09e-01 1.78e+01 ... (remaining 15764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 6590 16.16 - 32.33: 437 32.33 - 48.49: 90 48.49 - 64.66: 18 64.66 - 80.82: 14 Dihedral angle restraints: 7149 sinusoidal: 2845 harmonic: 4304 Sorted by residual: dihedral pdb=" CA ALA C 171 " pdb=" C ALA C 171 " pdb=" N ILE C 172 " pdb=" CA ILE C 172 " ideal model delta harmonic sigma weight residual 180.00 134.92 45.08 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" CA ASN C 217 " pdb=" C ASN C 217 " pdb=" N ILE C 218 " pdb=" CA ILE C 218 " ideal model delta harmonic sigma weight residual 180.00 -135.07 -44.93 0 5.00e+00 4.00e-02 8.07e+01 dihedral pdb=" CA SER C 164 " pdb=" C SER C 164 " pdb=" N VAL C 165 " pdb=" CA VAL C 165 " ideal model delta harmonic sigma weight residual 180.00 -135.25 -44.75 0 5.00e+00 4.00e-02 8.01e+01 ... (remaining 7146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1405 0.057 - 0.114: 407 0.114 - 0.171: 65 0.171 - 0.228: 4 0.228 - 0.285: 1 Chirality restraints: 1882 Sorted by residual: chirality pdb=" CA ASN C 217 " pdb=" N ASN C 217 " pdb=" C ASN C 217 " pdb=" CB ASN C 217 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE B 397 " pdb=" N ILE B 397 " pdb=" C ILE B 397 " pdb=" CB ILE B 397 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA ILE L 23 " pdb=" N ILE L 23 " pdb=" C ILE L 23 " pdb=" CB ILE L 23 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 1879 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 106 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO H 107 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 107 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 107 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 71 " 0.030 2.00e-02 2.50e+03 1.85e-02 6.87e+00 pdb=" CG TYR C 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 71 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 71 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 71 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 71 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 71 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 71 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 184 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 185 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " -0.033 5.00e-02 4.00e+02 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 173 2.61 - 3.18: 11225 3.18 - 3.76: 16719 3.76 - 4.33: 22617 4.33 - 4.90: 35791 Nonbonded interactions: 86525 Sorted by model distance: nonbonded pdb=" O TYR L 51 " pdb=" OG1 THR L 55 " model vdw 2.041 3.040 nonbonded pdb=" OG1 THR A 413 " pdb=" OE1 GLU A 416 " model vdw 2.047 3.040 nonbonded pdb=" O ALA B 150 " pdb=" OG1 THR B 154 " model vdw 2.070 3.040 nonbonded pdb=" OE2 GLU C 193 " pdb=" OG1 THR L 95 " model vdw 2.101 3.040 nonbonded pdb=" O LYS A 173 " pdb=" OH TYR A 235 " model vdw 2.155 3.040 ... (remaining 86520 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 84 or resid 124 through 215 or resid 226 throug \ h 260 or resid 263 through 472)) selection = (chain 'B' and (resid 20 through 84 or resid 124 through 472)) selection = (chain 'C' and (resid 20 through 215 or resid 226 through 260 or resid 263 throu \ gh 462 or (resid 463 and (name N or name CA or name C or name O or name CB )) or \ resid 464 through 472)) } 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: 2.040 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.500 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 11618 Z= 0.483 Angle : 1.015 9.447 15769 Z= 0.556 Chirality : 0.052 0.285 1882 Planarity : 0.006 0.075 2008 Dihedral : 11.746 80.819 4302 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.41 % Favored : 85.31 % Rotamer: Outliers : 0.38 % Allowed : 4.28 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -5.04 (0.18), residues: 1457 helix: -2.05 (0.22), residues: 359 sheet: -3.50 (0.32), residues: 180 loop : -4.12 (0.17), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 308 HIS 0.013 0.004 HIS L 91 PHE 0.033 0.003 PHE C 214 TYR 0.042 0.004 TYR C 71 ARG 0.013 0.002 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 332 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.5913 (mt) cc_final: 0.5659 (mt) REVERT: B 72 LYS cc_start: 0.6970 (mttt) cc_final: 0.6270 (mttt) REVERT: B 143 ASP cc_start: 0.5069 (m-30) cc_final: 0.4849 (m-30) REVERT: B 183 ILE cc_start: 0.8453 (tp) cc_final: 0.8221 (tp) REVERT: B 267 ILE cc_start: 0.5767 (pt) cc_final: 0.4754 (pt) REVERT: C 44 PHE cc_start: 0.4768 (t80) cc_final: 0.4537 (t80) REVERT: C 258 PHE cc_start: 0.6297 (t80) cc_final: 0.5829 (t80) outliers start: 5 outliers final: 1 residues processed: 337 average time/residue: 0.3043 time to fit residues: 137.0902 Evaluate side-chains 138 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.5980 chunk 109 optimal weight: 0.0670 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 113 optimal weight: 0.0030 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 139 GLN A 414 HIS B 26 GLN B 27 HIS B 206 HIS B 362 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 461 ASN C 43 ASN C 229 GLN C 418 ASN H 5 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11618 Z= 0.238 Angle : 0.781 10.058 15769 Z= 0.413 Chirality : 0.049 0.297 1882 Planarity : 0.006 0.074 2008 Dihedral : 7.459 46.427 1574 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.09 % Favored : 89.77 % Rotamer: Outliers : 0.38 % Allowed : 4.05 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.20), residues: 1457 helix: -0.79 (0.26), residues: 378 sheet: -3.17 (0.32), residues: 171 loop : -3.48 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.007 0.001 HIS L 91 PHE 0.015 0.002 PHE C 214 TYR 0.038 0.002 TYR C 71 ARG 0.007 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 231 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.5378 (t80) cc_final: 0.5066 (t80) REVERT: A 73 ARG cc_start: 0.5732 (ptp-170) cc_final: 0.5012 (mtt180) REVERT: B 149 GLU cc_start: 0.6062 (mt-10) cc_final: 0.5704 (mt-10) REVERT: C 44 PHE cc_start: 0.4872 (t80) cc_final: 0.4583 (t80) REVERT: L 90 CYS cc_start: 0.5866 (p) cc_final: 0.4709 (p) outliers start: 5 outliers final: 0 residues processed: 233 average time/residue: 0.2629 time to fit residues: 84.5092 Evaluate side-chains 122 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 130 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 279 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN B 198 GLN B 238 ASN B 403 GLN C 229 GLN C 279 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11618 Z= 0.326 Angle : 0.841 10.207 15769 Z= 0.442 Chirality : 0.051 0.253 1882 Planarity : 0.006 0.072 2008 Dihedral : 7.093 39.503 1574 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.81 % Favored : 88.13 % Rotamer: Outliers : 0.53 % Allowed : 5.04 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.20), residues: 1457 helix: -0.74 (0.25), residues: 394 sheet: -2.43 (0.32), residues: 204 loop : -3.39 (0.18), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 308 HIS 0.012 0.002 HIS L 91 PHE 0.016 0.003 PHE L 100 TYR 0.036 0.003 TYR C 71 ARG 0.005 0.001 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 1.401 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: A 56 LYS cc_start: 0.6365 (ttpt) cc_final: 0.6152 (ttpt) REVERT: A 71 TYR cc_start: 0.6340 (t80) cc_final: 0.5869 (t80) REVERT: A 255 ASP cc_start: 0.4694 (p0) cc_final: 0.4299 (p0) REVERT: B 198 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6453 (tm-30) REVERT: C 44 PHE cc_start: 0.5540 (t80) cc_final: 0.5189 (t80) REVERT: H 39 GLN cc_start: 0.7203 (pt0) cc_final: 0.6734 (pt0) outliers start: 7 outliers final: 1 residues processed: 189 average time/residue: 0.2493 time to fit residues: 66.8618 Evaluate side-chains 111 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 0.0470 chunk 62 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 395 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN C 217 ASN C 279 GLN C 447 ASN H 77 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11618 Z= 0.203 Angle : 0.712 9.585 15769 Z= 0.372 Chirality : 0.047 0.223 1882 Planarity : 0.005 0.062 2008 Dihedral : 6.536 36.849 1574 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.78 % Favored : 89.16 % Rotamer: Outliers : 0.15 % Allowed : 4.43 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.21), residues: 1457 helix: -0.34 (0.26), residues: 382 sheet: -1.70 (0.34), residues: 191 loop : -3.15 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 37 HIS 0.003 0.001 HIS L 91 PHE 0.015 0.002 PHE C 346 TYR 0.033 0.002 TYR L 93 ARG 0.009 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6555 (t80) cc_final: 0.6045 (t80) REVERT: A 255 ASP cc_start: 0.4647 (p0) cc_final: 0.4293 (p0) REVERT: A 449 VAL cc_start: 0.7440 (m) cc_final: 0.7218 (m) REVERT: C 44 PHE cc_start: 0.5196 (t80) cc_final: 0.4920 (t80) REVERT: L 90 CYS cc_start: 0.5542 (p) cc_final: 0.4708 (p) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.2371 time to fit residues: 60.0495 Evaluate side-chains 118 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 176 GLN B 414 HIS C 206 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.7984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11618 Z= 0.328 Angle : 0.813 12.637 15769 Z= 0.425 Chirality : 0.049 0.210 1882 Planarity : 0.005 0.063 2008 Dihedral : 6.876 36.995 1574 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.77 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.20), residues: 1457 helix: -0.69 (0.25), residues: 394 sheet: -1.97 (0.33), residues: 209 loop : -3.07 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 37 HIS 0.010 0.003 HIS C 27 PHE 0.018 0.002 PHE B 258 TYR 0.038 0.003 TYR C 71 ARG 0.005 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.269 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: A 227 LYS cc_start: 0.8127 (tttp) cc_final: 0.7750 (ttmt) REVERT: A 317 MET cc_start: 0.7526 (mpp) cc_final: 0.7296 (mpp) REVERT: B 352 MET cc_start: 0.7534 (ttm) cc_final: 0.7067 (ttp) REVERT: C 44 PHE cc_start: 0.5308 (t80) cc_final: 0.4848 (t80) REVERT: C 348 LEU cc_start: 0.8027 (mp) cc_final: 0.7514 (mp) REVERT: H 57 THR cc_start: 0.4462 (p) cc_final: 0.4260 (p) REVERT: L 92 GLN cc_start: 0.8049 (pt0) cc_final: 0.7766 (pt0) REVERT: L 98 ILE cc_start: 0.8957 (mm) cc_final: 0.8683 (tt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2502 time to fit residues: 57.0125 Evaluate side-chains 104 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.8743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11618 Z= 0.273 Angle : 0.770 9.735 15769 Z= 0.401 Chirality : 0.048 0.225 1882 Planarity : 0.005 0.060 2008 Dihedral : 6.657 36.179 1574 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.19 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.21), residues: 1457 helix: -0.47 (0.27), residues: 368 sheet: -1.92 (0.33), residues: 215 loop : -2.89 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 103 HIS 0.004 0.001 HIS C 414 PHE 0.014 0.002 PHE B 258 TYR 0.043 0.003 TYR C 71 ARG 0.006 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.425 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: C 302 ASN cc_start: 0.8544 (t0) cc_final: 0.8317 (t0) REVERT: H 57 THR cc_start: 0.4514 (p) cc_final: 0.4295 (p) REVERT: L 6 MET cc_start: 0.8009 (ppp) cc_final: 0.7297 (ppp) REVERT: L 96 TYR cc_start: 0.7280 (t80) cc_final: 0.7044 (t80) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2679 time to fit residues: 58.9015 Evaluate side-chains 100 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 118 optimal weight: 0.0070 chunk 78 optimal weight: 0.0670 chunk 139 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.9023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11618 Z= 0.196 Angle : 0.727 8.780 15769 Z= 0.376 Chirality : 0.048 0.254 1882 Planarity : 0.005 0.056 2008 Dihedral : 6.371 34.647 1574 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.02 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.21), residues: 1457 helix: -0.41 (0.27), residues: 370 sheet: -1.71 (0.35), residues: 210 loop : -2.82 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP L 37 HIS 0.004 0.001 HIS L 91 PHE 0.036 0.002 PHE A 243 TYR 0.031 0.002 TYR C 71 ARG 0.006 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.301 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: A 317 MET cc_start: 0.7550 (mpp) cc_final: 0.7284 (mpp) REVERT: C 302 ASN cc_start: 0.8506 (t0) cc_final: 0.8186 (t0) REVERT: H 21 THR cc_start: 0.7271 (p) cc_final: 0.7049 (p) REVERT: H 57 THR cc_start: 0.4565 (p) cc_final: 0.4191 (p) REVERT: H 59 TYR cc_start: 0.5952 (m-10) cc_final: 0.5740 (m-80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2467 time to fit residues: 53.9727 Evaluate side-chains 103 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.0070 chunk 83 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 0.0270 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 109 optimal weight: 0.0170 chunk 127 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.9276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11618 Z= 0.183 Angle : 0.716 8.584 15769 Z= 0.370 Chirality : 0.047 0.209 1882 Planarity : 0.004 0.053 2008 Dihedral : 6.047 32.916 1574 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.33 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.21), residues: 1457 helix: -0.44 (0.26), residues: 381 sheet: -1.43 (0.36), residues: 204 loop : -2.84 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 37 HIS 0.003 0.001 HIS A 27 PHE 0.026 0.001 PHE A 243 TYR 0.036 0.002 TYR C 71 ARG 0.007 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.7378 (mpp) cc_final: 0.7142 (mpp) REVERT: C 302 ASN cc_start: 0.8446 (t0) cc_final: 0.8155 (t0) REVERT: H 57 THR cc_start: 0.4767 (p) cc_final: 0.4460 (p) REVERT: H 59 TYR cc_start: 0.5915 (m-10) cc_final: 0.5709 (m-80) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2500 time to fit residues: 53.5046 Evaluate side-chains 96 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 0.0050 chunk 133 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.9482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11618 Z= 0.202 Angle : 0.720 8.918 15769 Z= 0.372 Chirality : 0.047 0.215 1882 Planarity : 0.004 0.051 2008 Dihedral : 6.085 32.552 1574 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.21), residues: 1457 helix: -0.39 (0.26), residues: 387 sheet: -1.35 (0.36), residues: 200 loop : -2.81 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 37 HIS 0.008 0.001 HIS C 27 PHE 0.021 0.002 PHE A 243 TYR 0.029 0.002 TYR B 254 ARG 0.007 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.333 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: A 317 MET cc_start: 0.7271 (mpp) cc_final: 0.7057 (mpp) REVERT: C 302 ASN cc_start: 0.8462 (t0) cc_final: 0.8203 (t0) REVERT: H 57 THR cc_start: 0.5098 (p) cc_final: 0.4698 (p) REVERT: L 87 THR cc_start: 0.8511 (m) cc_final: 0.7972 (p) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2520 time to fit residues: 53.2035 Evaluate side-chains 105 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 144 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.9847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11618 Z= 0.220 Angle : 0.740 9.965 15769 Z= 0.383 Chirality : 0.047 0.210 1882 Planarity : 0.004 0.051 2008 Dihedral : 6.121 32.673 1574 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.21), residues: 1457 helix: -0.36 (0.26), residues: 382 sheet: -1.37 (0.36), residues: 202 loop : -2.78 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 37 HIS 0.007 0.002 HIS C 27 PHE 0.019 0.002 PHE A 243 TYR 0.029 0.002 TYR B 254 ARG 0.008 0.001 ARG L 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.7394 (mpp) cc_final: 0.7031 (mpp) REVERT: B 38 MET cc_start: 0.7813 (tpt) cc_final: 0.7269 (tpt) REVERT: C 44 PHE cc_start: 0.5077 (t80) cc_final: 0.4792 (t80) REVERT: C 302 ASN cc_start: 0.8404 (t0) cc_final: 0.8164 (t0) REVERT: C 348 LEU cc_start: 0.7849 (mp) cc_final: 0.7152 (mp) REVERT: H 57 THR cc_start: 0.5133 (p) cc_final: 0.4778 (p) REVERT: H 97 ARG cc_start: 0.5472 (ttt-90) cc_final: 0.4548 (ttp80) REVERT: L 87 THR cc_start: 0.8583 (m) cc_final: 0.8025 (p) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2625 time to fit residues: 52.7224 Evaluate side-chains 104 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 101 optimal weight: 0.0060 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.098726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.088814 restraints weight = 41767.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.090586 restraints weight = 28040.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.091881 restraints weight = 20479.027| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 1.0012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11618 Z= 0.198 Angle : 0.714 9.600 15769 Z= 0.369 Chirality : 0.047 0.207 1882 Planarity : 0.004 0.049 2008 Dihedral : 5.982 32.229 1574 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1457 helix: -0.36 (0.26), residues: 394 sheet: -1.32 (0.36), residues: 205 loop : -2.74 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 37 HIS 0.006 0.001 HIS C 315 PHE 0.017 0.001 PHE A 243 TYR 0.035 0.002 TYR C 71 ARG 0.008 0.001 ARG L 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.37 seconds wall clock time: 45 minutes 12.38 seconds (2712.38 seconds total)