Starting phenix.real_space_refine on Tue Jun 10 04:15:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mjz_9135/06_2025/6mjz_9135.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mjz_9135/06_2025/6mjz_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_9135/06_2025/6mjz_9135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mjz_9135/06_2025/6mjz_9135.map" model { file = "/net/cci-nas-00/data/ceres_data/6mjz_9135/06_2025/6mjz_9135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mjz_9135/06_2025/6mjz_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-5710/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: 6.99, per 1000 atoms: 0.61 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 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: 1.21 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: 3.22 Time building geometry restraints manager: 3.00 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: 2.440 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.820 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- 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 : 0.018 0.807 11641 Z= 0.897 Angle : 1.094 33.850 15815 Z= 0.589 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 Details of bonding type rmsd hydrogen bonds : bond 0.16422 ( 349) hydrogen bonds : angle 7.93878 ( 948) SS BOND : bond 0.37727 ( 23) SS BOND : angle 7.65423 ( 46) covalent geometry : bond 0.00746 (11618) covalent geometry : angle 1.01475 (15769) *********************** 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 : 1.240 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: 0.2943 time to fit residues: 132.0953 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 : 1.348 ------------------------------------------------------------------------------- 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: 0.0270 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 113 optimal weight: 0.0030 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.4248 ------------------------------------------------------------------------------- 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 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 418 ASN H 5 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.104542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.095283 restraints weight = 41122.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.097003 restraints weight = 27902.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.098261 restraints weight = 20231.248| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11641 Z= 0.163 Angle : 0.788 10.352 15815 Z= 0.416 Chirality : 0.049 0.296 1882 Planarity : 0.006 0.073 2008 Dihedral : 7.525 46.211 1574 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.95 % Favored : 89.91 % Rotamer: Outliers : 0.38 % Allowed : 4.13 % Favored : 95.49 % 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: -3.93 (0.20), residues: 1457 helix: -0.81 (0.26), residues: 378 sheet: -3.07 (0.32), residues: 176 loop : -3.54 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.007 0.001 HIS L 91 PHE 0.015 0.002 PHE B 346 TYR 0.037 0.002 TYR C 71 ARG 0.008 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 349) hydrogen bonds : angle 5.97689 ( 948) SS BOND : bond 0.00495 ( 23) SS BOND : angle 1.78774 ( 46) covalent geometry : bond 0.00367 (11618) covalent geometry : angle 0.78280 (15769) *********************** 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 237 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 232 time to evaluate : 1.406 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: 0.6386 (t80) cc_final: 0.5956 (t80) REVERT: A 73 ARG cc_start: 0.6523 (ptp-110) cc_final: 0.5786 (mtt180) REVERT: A 135 VAL cc_start: 0.8409 (p) cc_final: 0.8156 (m) REVERT: B 58 GLU cc_start: 0.6985 (mp0) cc_final: 0.6775 (mp0) REVERT: B 149 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6579 (mt-10) REVERT: C 40 ILE cc_start: 0.6743 (mt) cc_final: 0.6483 (mt) REVERT: C 44 PHE cc_start: 0.5348 (t80) cc_final: 0.4929 (t80) REVERT: C 156 LYS cc_start: 0.6963 (mmtt) cc_final: 0.6642 (mmtt) REVERT: L 81 GLN cc_start: 0.6490 (mp-120) cc_final: 0.6282 (mp-120) REVERT: L 90 CYS cc_start: 0.5831 (p) cc_final: 0.4405 (p) REVERT: L 98 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7265 (tp) outliers start: 5 outliers final: 0 residues processed: 234 average time/residue: 0.2644 time to fit residues: 85.6649 Evaluate side-chains 124 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 49 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 238 ASN B 403 GLN B 461 ASN C 43 ASN C 229 GLN L 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.100840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.091103 restraints weight = 41366.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.092946 restraints weight = 27521.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.094264 restraints weight = 19724.838| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11641 Z= 0.208 Angle : 0.822 9.660 15815 Z= 0.431 Chirality : 0.050 0.248 1882 Planarity : 0.006 0.068 2008 Dihedral : 6.980 39.377 1574 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.12 % Favored : 88.81 % Rotamer: Outliers : 0.31 % Allowed : 4.66 % Favored : 95.03 % 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: -3.52 (0.20), residues: 1457 helix: -0.48 (0.26), residues: 382 sheet: -2.48 (0.32), residues: 209 loop : -3.37 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 47 HIS 0.012 0.002 HIS A 350 PHE 0.015 0.002 PHE L 100 TYR 0.036 0.003 TYR C 71 ARG 0.009 0.001 ARG L 20 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 349) hydrogen bonds : angle 5.71807 ( 948) SS BOND : bond 0.00846 ( 23) SS BOND : angle 1.97012 ( 46) covalent geometry : bond 0.00466 (11618) covalent geometry : angle 0.81677 (15769) *********************** 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 198 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 194 time to evaluate : 1.341 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: A 56 LYS cc_start: 0.6759 (ttpt) cc_final: 0.6445 (ttpt) REVERT: A 135 VAL cc_start: 0.8551 (p) cc_final: 0.8274 (m) REVERT: A 255 ASP cc_start: 0.6917 (p0) cc_final: 0.6403 (p0) REVERT: A 265 ARG cc_start: 0.6857 (mmt-90) cc_final: 0.6449 (tpp80) REVERT: A 353 GLU cc_start: 0.6702 (mp0) cc_final: 0.6329 (mp0) REVERT: B 79 ILE cc_start: 0.8825 (mm) cc_final: 0.8615 (mm) REVERT: B 209 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7213 (tp30) REVERT: B 425 MET cc_start: 0.6031 (mtt) cc_final: 0.4951 (mtm) REVERT: C 44 PHE cc_start: 0.5939 (t80) cc_final: 0.5397 (t80) REVERT: C 159 GLN cc_start: 0.6099 (mt0) cc_final: 0.5783 (mm-40) REVERT: C 378 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.6474 (m-10) REVERT: H 93 TYR cc_start: 0.6755 (m-80) cc_final: 0.6368 (m-80) outliers start: 4 outliers final: 2 residues processed: 198 average time/residue: 0.2460 time to fit residues: 70.5723 Evaluate side-chains 115 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 C 217 ASN H 81 ASN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.101136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.091480 restraints weight = 41575.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.093320 restraints weight = 27504.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.094642 restraints weight = 19691.777| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11641 Z= 0.151 Angle : 0.732 9.231 15815 Z= 0.384 Chirality : 0.047 0.229 1882 Planarity : 0.005 0.061 2008 Dihedral : 6.584 37.501 1574 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.57 % Favored : 89.36 % Rotamer: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.19 % 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: -3.24 (0.20), residues: 1457 helix: -0.43 (0.26), residues: 391 sheet: -2.14 (0.33), residues: 203 loop : -3.16 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 37 HIS 0.005 0.001 HIS L 91 PHE 0.022 0.002 PHE B 427 TYR 0.032 0.002 TYR C 71 ARG 0.005 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 349) hydrogen bonds : angle 5.38237 ( 948) SS BOND : bond 0.00416 ( 23) SS BOND : angle 1.60661 ( 46) covalent geometry : bond 0.00345 (11618) covalent geometry : angle 0.72825 (15769) *********************** 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 172 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 1.382 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: A 135 VAL cc_start: 0.8605 (p) cc_final: 0.8300 (m) REVERT: A 227 LYS cc_start: 0.8408 (tttp) cc_final: 0.8186 (ttmt) REVERT: A 255 ASP cc_start: 0.6757 (p0) cc_final: 0.6340 (p0) REVERT: A 265 ARG cc_start: 0.6933 (mmt-90) cc_final: 0.6612 (tpp80) REVERT: A 317 MET cc_start: 0.7384 (mpp) cc_final: 0.7058 (mpp) REVERT: B 209 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7206 (tp30) REVERT: C 44 PHE cc_start: 0.5962 (t80) cc_final: 0.5352 (t80) REVERT: C 348 LEU cc_start: 0.8455 (mt) cc_final: 0.8189 (mt) REVERT: H 93 TYR cc_start: 0.6899 (m-80) cc_final: 0.6539 (m-80) REVERT: L 90 CYS cc_start: 0.5574 (p) cc_final: 0.4466 (p) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.2187 time to fit residues: 54.6099 Evaluate side-chains 119 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.0060 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN B 414 HIS C 206 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.095799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.085894 restraints weight = 41856.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.087647 restraints weight = 28003.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088941 restraints weight = 20331.282| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.8250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 11641 Z= 0.245 Angle : 0.863 11.296 15815 Z= 0.455 Chirality : 0.050 0.246 1882 Planarity : 0.006 0.065 2008 Dihedral : 7.108 37.665 1574 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.38 % Favored : 86.55 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -3.39 (0.20), residues: 1457 helix: -0.82 (0.25), residues: 382 sheet: -2.15 (0.33), residues: 201 loop : -3.12 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 308 HIS 0.011 0.003 HIS C 27 PHE 0.019 0.003 PHE B 258 TYR 0.035 0.003 TYR C 71 ARG 0.008 0.001 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 349) hydrogen bonds : angle 5.85838 ( 948) SS BOND : bond 0.00403 ( 23) SS BOND : angle 1.96577 ( 46) covalent geometry : bond 0.00575 (11618) covalent geometry : angle 0.85816 (15769) *********************** 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 171 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.357 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 255 ASP cc_start: 0.6815 (p0) cc_final: 0.6553 (p0) REVERT: A 317 MET cc_start: 0.7455 (mpp) cc_final: 0.7010 (mpp) REVERT: A 353 GLU cc_start: 0.6941 (mp0) cc_final: 0.6546 (mp0) REVERT: B 58 GLU cc_start: 0.7338 (mp0) cc_final: 0.7060 (mp0) REVERT: B 425 MET cc_start: 0.6028 (mtt) cc_final: 0.5516 (mtm) REVERT: H 17 THR cc_start: 0.6109 (m) cc_final: 0.5862 (p) REVERT: H 21 THR cc_start: 0.7906 (p) cc_final: 0.7601 (p) REVERT: H 93 TYR cc_start: 0.7949 (m-80) cc_final: 0.7537 (m-80) REVERT: L 47 LYS cc_start: 0.6551 (pttm) cc_final: 0.6205 (pttt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2637 time to fit residues: 64.7680 Evaluate side-chains 107 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 139 optimal weight: 0.0020 chunk 61 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.099729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.089630 restraints weight = 41625.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.091478 restraints weight = 27415.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092848 restraints weight = 19739.593| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.8544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11641 Z= 0.141 Angle : 0.747 10.015 15815 Z= 0.389 Chirality : 0.047 0.208 1882 Planarity : 0.005 0.059 2008 Dihedral : 6.509 35.389 1574 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.36 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -3.20 (0.20), residues: 1457 helix: -0.69 (0.26), residues: 384 sheet: -2.05 (0.34), residues: 201 loop : -2.98 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 103 HIS 0.008 0.001 HIS L 91 PHE 0.025 0.002 PHE C 346 TYR 0.045 0.002 TYR C 71 ARG 0.011 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 349) hydrogen bonds : angle 5.40433 ( 948) SS BOND : bond 0.00429 ( 23) SS BOND : angle 1.61466 ( 46) covalent geometry : bond 0.00323 (11618) covalent geometry : angle 0.74297 (15769) *********************** 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 170 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.311 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 317 MET cc_start: 0.7372 (mpp) cc_final: 0.6871 (mpp) REVERT: A 456 ILE cc_start: 0.8112 (mp) cc_final: 0.7823 (mp) REVERT: B 58 GLU cc_start: 0.7244 (mp0) cc_final: 0.6882 (mp0) REVERT: B 352 MET cc_start: 0.7880 (ttm) cc_final: 0.7640 (ttp) REVERT: B 425 MET cc_start: 0.6082 (mtt) cc_final: 0.5860 (mtm) REVERT: C 44 PHE cc_start: 0.6003 (t80) cc_final: 0.5731 (t80) REVERT: C 156 LYS cc_start: 0.6597 (mmtm) cc_final: 0.5896 (mmtm) REVERT: C 455 ASP cc_start: 0.7985 (m-30) cc_final: 0.7687 (m-30) REVERT: H 93 TYR cc_start: 0.7426 (m-80) cc_final: 0.7146 (m-80) REVERT: H 97 ARG cc_start: 0.5590 (ttt180) cc_final: 0.4967 (ttp80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2716 time to fit residues: 66.5273 Evaluate side-chains 111 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 144 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 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 = 0.3780 r_free = 0.3780 target = 0.095935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085805 restraints weight = 42395.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.087598 restraints weight = 28242.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.088888 restraints weight = 20407.226| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.9161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11641 Z= 0.195 Angle : 0.802 8.943 15815 Z= 0.417 Chirality : 0.049 0.234 1882 Planarity : 0.005 0.061 2008 Dihedral : 6.665 35.569 1574 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.11 % Favored : 86.82 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -3.24 (0.20), residues: 1457 helix: -0.80 (0.26), residues: 377 sheet: -1.86 (0.34), residues: 210 loop : -3.01 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 103 HIS 0.006 0.002 HIS A 27 PHE 0.017 0.002 PHE B 258 TYR 0.049 0.003 TYR C 71 ARG 0.011 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 349) hydrogen bonds : angle 5.56266 ( 948) SS BOND : bond 0.00506 ( 23) SS BOND : angle 1.74998 ( 46) covalent geometry : bond 0.00455 (11618) covalent geometry : angle 0.79732 (15769) *********************** 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 147 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.224 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 317 MET cc_start: 0.7378 (mpp) cc_final: 0.6859 (mpp) REVERT: A 420 ILE cc_start: 0.6519 (mt) cc_final: 0.6233 (tt) REVERT: B 352 MET cc_start: 0.8110 (ttm) cc_final: 0.7786 (ttp) REVERT: C 348 LEU cc_start: 0.8810 (mt) cc_final: 0.8571 (mt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2078 time to fit residues: 45.2071 Evaluate side-chains 101 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 102 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 279 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 = 0.3793 r_free = 0.3793 target = 0.096531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.086763 restraints weight = 42482.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.088579 restraints weight = 27940.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.089879 restraints weight = 20070.423| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.9490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11641 Z= 0.164 Angle : 0.769 8.679 15815 Z= 0.400 Chirality : 0.048 0.211 1882 Planarity : 0.005 0.052 2008 Dihedral : 6.488 34.293 1574 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.98 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -3.14 (0.21), residues: 1457 helix: -0.78 (0.26), residues: 377 sheet: -1.86 (0.35), residues: 211 loop : -2.90 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 111 HIS 0.004 0.001 HIS C 206 PHE 0.038 0.002 PHE A 243 TYR 0.042 0.002 TYR L 93 ARG 0.012 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 349) hydrogen bonds : angle 5.50338 ( 948) SS BOND : bond 0.00598 ( 23) SS BOND : angle 1.79585 ( 46) covalent geometry : bond 0.00379 (11618) covalent geometry : angle 0.76421 (15769) *********************** 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 151 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.314 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: symmetry clash REVERT: A 38 MET cc_start: 0.7322 (ttt) cc_final: 0.6968 (ttt) REVERT: A 44 PHE cc_start: 0.7268 (m-10) cc_final: 0.6962 (m-10) REVERT: A 317 MET cc_start: 0.7494 (mpp) cc_final: 0.7144 (mpp) REVERT: A 420 ILE cc_start: 0.6675 (mt) cc_final: 0.6275 (tt) REVERT: B 352 MET cc_start: 0.8017 (ttm) cc_final: 0.7733 (ttp) REVERT: C 348 LEU cc_start: 0.8786 (mt) cc_final: 0.8469 (mt) REVERT: C 455 ASP cc_start: 0.8104 (m-30) cc_final: 0.7872 (m-30) REVERT: L 85 PHE cc_start: 0.7780 (t80) cc_final: 0.7532 (t80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2412 time to fit residues: 52.1501 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 : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 69 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 121 optimal weight: 0.0070 chunk 132 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.098017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.088114 restraints weight = 42251.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.089946 restraints weight = 28127.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.091262 restraints weight = 20252.723| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.9699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11641 Z= 0.138 Angle : 0.752 8.618 15815 Z= 0.391 Chirality : 0.048 0.205 1882 Planarity : 0.005 0.055 2008 Dihedral : 6.292 33.465 1574 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.91 % Favored : 89.02 % Rotamer: Outliers : 0.08 % Allowed : 0.84 % Favored : 99.08 % 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: -3.01 (0.21), residues: 1457 helix: -0.70 (0.26), residues: 376 sheet: -1.63 (0.36), residues: 205 loop : -2.83 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 103 HIS 0.003 0.001 HIS A 27 PHE 0.031 0.002 PHE A 243 TYR 0.045 0.002 TYR C 71 ARG 0.013 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 349) hydrogen bonds : angle 5.43068 ( 948) SS BOND : bond 0.00394 ( 23) SS BOND : angle 1.94009 ( 46) covalent geometry : bond 0.00313 (11618) covalent geometry : angle 0.74566 (15769) *********************** 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 152 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.820 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 38 MET cc_start: 0.7368 (ttt) cc_final: 0.7020 (ttt) REVERT: A 44 PHE cc_start: 0.7275 (m-10) cc_final: 0.6979 (m-10) REVERT: A 317 MET cc_start: 0.7445 (mpp) cc_final: 0.7070 (mpp) REVERT: A 420 ILE cc_start: 0.6623 (mt) cc_final: 0.6264 (tt) REVERT: B 38 MET cc_start: 0.7939 (tpt) cc_final: 0.7738 (tpt) REVERT: B 352 MET cc_start: 0.7894 (ttm) cc_final: 0.7582 (ttp) REVERT: C 352 MET cc_start: 0.8190 (tpp) cc_final: 0.7848 (tpp) REVERT: C 455 ASP cc_start: 0.8152 (m-30) cc_final: 0.7898 (m-30) REVERT: L 85 PHE cc_start: 0.7692 (t80) cc_final: 0.7400 (t80) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.2891 time to fit residues: 63.5213 Evaluate side-chains 99 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 39 optimal weight: 0.0000 overall best weight: 0.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 279 GLN ** C 407 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 = 0.3832 r_free = 0.3832 target = 0.098606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.088840 restraints weight = 41505.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.090637 restraints weight = 27324.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.091948 restraints weight = 19686.458| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.9863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11641 Z= 0.143 Angle : 0.785 22.502 15815 Z= 0.399 Chirality : 0.048 0.275 1882 Planarity : 0.005 0.058 2008 Dihedral : 6.299 32.523 1574 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.91 % Favored : 88.95 % Rotamer: Outliers : 0.08 % Allowed : 0.15 % Favored : 99.77 % 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: -2.92 (0.21), residues: 1457 helix: -0.63 (0.26), residues: 376 sheet: -1.36 (0.38), residues: 198 loop : -2.83 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 37 HIS 0.007 0.001 HIS C 27 PHE 0.029 0.002 PHE A 243 TYR 0.032 0.002 TYR C 71 ARG 0.015 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 349) hydrogen bonds : angle 5.35131 ( 948) SS BOND : bond 0.00386 ( 23) SS BOND : angle 2.50058 ( 46) covalent geometry : bond 0.00325 (11618) covalent geometry : angle 0.77398 (15769) ********************** 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 145 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.365 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 317 MET cc_start: 0.7390 (mpp) cc_final: 0.6835 (mpp) REVERT: A 420 ILE cc_start: 0.6626 (mt) cc_final: 0.6290 (tt) REVERT: B 352 MET cc_start: 0.7771 (ttm) cc_final: 0.7459 (ttp) REVERT: C 28 VAL cc_start: 0.8510 (m) cc_final: 0.8212 (p) REVERT: C 455 ASP cc_start: 0.8109 (m-30) cc_final: 0.7845 (m-30) REVERT: L 85 PHE cc_start: 0.7621 (t80) cc_final: 0.7333 (t80) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.2637 time to fit residues: 53.9213 Evaluate side-chains 101 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 140 optimal weight: 0.0470 chunk 135 optimal weight: 2.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 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 = 0.3814 r_free = 0.3814 target = 0.097668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087774 restraints weight = 41843.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.089558 restraints weight = 27997.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.090871 restraints weight = 20252.426| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 1.0050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11641 Z= 0.157 Angle : 0.779 21.305 15815 Z= 0.397 Chirality : 0.048 0.334 1882 Planarity : 0.005 0.053 2008 Dihedral : 6.259 32.699 1574 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.67 % Favored : 88.26 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -2.88 (0.21), residues: 1457 helix: -0.61 (0.26), residues: 378 sheet: -1.30 (0.38), residues: 197 loop : -2.81 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 103 HIS 0.005 0.001 HIS A 27 PHE 0.029 0.002 PHE A 243 TYR 0.035 0.002 TYR C 71 ARG 0.007 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 349) hydrogen bonds : angle 5.30324 ( 948) SS BOND : bond 0.00420 ( 23) SS BOND : angle 2.34847 ( 46) covalent geometry : bond 0.00362 (11618) covalent geometry : angle 0.76927 (15769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.00 seconds wall clock time: 61 minutes 51.71 seconds (3711.71 seconds total)