Starting phenix.real_space_refine on Wed Mar 4 05:49:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mjz_9135/03_2026/6mjz_9135.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mjz_9135/03_2026/6mjz_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 { model { file = "/net/cci-nas-00/data/ceres_data/6mjz_9135/03_2026/6mjz_9135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mjz_9135/03_2026/6mjz_9135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mjz_9135/03_2026/6mjz_9135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mjz_9135/03_2026/6mjz_9135.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.60, per 1000 atoms: 0.23 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: 0.96 Conformation dependent library (CDL) restraints added in 532.4 milliseconds 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: 0.38 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: 1.64 Time building geometry restraints manager: 1.33 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: 1.960 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.000 ------------------------------------------------------------------------------- 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 : 7.75 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.002 ARG B 265 TYR 0.042 0.004 TYR C 71 PHE 0.033 0.003 PHE C 214 TRP 0.015 0.002 TRP B 308 HIS 0.013 0.004 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00746 (11618) covalent geometry : angle 1.01475 (15769) SS BOND : bond 0.37727 ( 23) SS BOND : angle 7.65423 ( 46) hydrogen bonds : bond 0.16422 ( 349) hydrogen bonds : angle 7.93878 ( 948) *********************** 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 : 0.433 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: 0.5067 (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: 0.5768 (pt) cc_final: 0.4754 (pt) REVERT: C 44 PHE cc_start: 0.4769 (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: 0.1312 time to fit residues: 59.2620 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 : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 395 ASN A 414 HIS B 26 GLN B 27 HIS B 206 HIS B 362 GLN B 403 GLN B 447 ASN B 461 ASN C 43 ASN C 418 ASN H 5 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.103600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.094121 restraints weight = 41243.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.095841 restraints weight = 28073.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.097138 restraints weight = 20338.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.098068 restraints weight = 15525.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.098711 restraints weight = 12372.895| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11641 Z= 0.171 Angle : 0.794 9.906 15815 Z= 0.420 Chirality : 0.050 0.301 1882 Planarity : 0.006 0.076 2008 Dihedral : 7.442 46.876 1574 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.09 % Favored : 89.77 % Rotamer: Outliers : 0.38 % Allowed : 4.35 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.20), residues: 1457 helix: -0.76 (0.26), residues: 378 sheet: -2.88 (0.31), residues: 203 loop : -3.53 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 105 TYR 0.038 0.002 TYR C 71 PHE 0.016 0.002 PHE C 214 TRP 0.011 0.002 TRP H 47 HIS 0.008 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00387 (11618) covalent geometry : angle 0.78964 (15769) SS BOND : bond 0.00446 ( 23) SS BOND : angle 1.80417 ( 46) hydrogen bonds : bond 0.04676 ( 349) hydrogen bonds : angle 5.88906 ( 948) *********************** 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 228 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 223 time to evaluate : 0.395 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 71 TYR cc_start: 0.6671 (t80) cc_final: 0.6127 (t80) REVERT: A 73 ARG cc_start: 0.6713 (ptp-110) cc_final: 0.5922 (mtt180) REVERT: A 135 VAL cc_start: 0.8392 (p) cc_final: 0.8104 (m) REVERT: A 317 MET cc_start: 0.5306 (ptm) cc_final: 0.4848 (ptm) REVERT: B 149 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6629 (mt-10) REVERT: B 425 MET cc_start: 0.5558 (mtt) cc_final: 0.5237 (mtt) REVERT: C 40 ILE cc_start: 0.6955 (mt) cc_final: 0.6636 (mt) REVERT: C 44 PHE cc_start: 0.5399 (t80) cc_final: 0.4924 (t80) REVERT: C 156 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6679 (mmtt) REVERT: C 452 ASP cc_start: 0.6624 (t0) cc_final: 0.6047 (t0) REVERT: L 90 CYS cc_start: 0.5695 (p) cc_final: 0.4155 (p) REVERT: L 98 ILE cc_start: 0.7864 (tp) cc_final: 0.7590 (tp) outliers start: 5 outliers final: 0 residues processed: 226 average time/residue: 0.1228 time to fit residues: 38.3436 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 : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 5 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8904 ------------------------------------------------------------------------------- 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** B 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.101670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091818 restraints weight = 41570.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.093644 restraints weight = 27916.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.095031 restraints weight = 20067.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.096008 restraints weight = 15174.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.096783 restraints weight = 12037.020| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11641 Z= 0.177 Angle : 0.759 9.654 15815 Z= 0.398 Chirality : 0.048 0.260 1882 Planarity : 0.005 0.067 2008 Dihedral : 6.728 38.124 1574 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.50 % Favored : 89.43 % Rotamer: Outliers : 0.31 % Allowed : 4.13 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.20), residues: 1457 helix: -0.40 (0.27), residues: 379 sheet: -2.39 (0.30), residues: 219 loop : -3.35 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 236 TYR 0.036 0.002 TYR C 71 PHE 0.018 0.002 PHE L 100 TRP 0.009 0.002 TRP H 47 HIS 0.009 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00404 (11618) covalent geometry : angle 0.75235 (15769) SS BOND : bond 0.01317 ( 23) SS BOND : angle 1.93924 ( 46) hydrogen bonds : bond 0.04528 ( 349) hydrogen bonds : angle 5.49597 ( 948) *********************** 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 195 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 0.445 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 135 VAL cc_start: 0.8409 (p) cc_final: 0.8033 (m) REVERT: A 265 ARG cc_start: 0.6872 (mmt-90) cc_final: 0.6467 (tpp80) REVERT: B 79 ILE cc_start: 0.8804 (mm) cc_final: 0.8584 (mm) REVERT: B 227 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7601 (mmtp) REVERT: C 44 PHE cc_start: 0.5862 (t80) cc_final: 0.5343 (t80) REVERT: C 159 GLN cc_start: 0.5973 (mt0) cc_final: 0.5733 (mm-40) REVERT: C 452 ASP cc_start: 0.6694 (t0) cc_final: 0.6277 (t0) REVERT: H 70 SER cc_start: 0.4821 (p) cc_final: 0.4571 (m) REVERT: H 93 TYR cc_start: 0.6638 (m-80) cc_final: 0.6414 (m-80) outliers start: 4 outliers final: 2 residues processed: 193 average time/residue: 0.1078 time to fit residues: 29.8531 Evaluate side-chains 113 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.0270 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 59 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.102589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092810 restraints weight = 41151.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.094724 restraints weight = 27202.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.096117 restraints weight = 19397.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.097144 restraints weight = 14542.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.097842 restraints weight = 11364.639| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11641 Z= 0.131 Angle : 0.701 8.844 15815 Z= 0.366 Chirality : 0.046 0.220 1882 Planarity : 0.005 0.063 2008 Dihedral : 6.324 36.293 1574 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.61 % Favored : 90.32 % Rotamer: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.21), residues: 1457 helix: -0.18 (0.27), residues: 373 sheet: -1.95 (0.33), residues: 211 loop : -3.08 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 105 TYR 0.032 0.002 TYR C 71 PHE 0.011 0.001 PHE L 100 TRP 0.012 0.001 TRP L 37 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00294 (11618) covalent geometry : angle 0.69694 (15769) SS BOND : bond 0.00400 ( 23) SS BOND : angle 1.54943 ( 46) hydrogen bonds : bond 0.03942 ( 349) hydrogen bonds : angle 5.23641 ( 948) *********************** 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 179 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.531 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: 0.7228 (t80) cc_final: 0.6918 (t80) REVERT: A 135 VAL cc_start: 0.8432 (p) cc_final: 0.8038 (m) REVERT: A 265 ARG cc_start: 0.6999 (mmt-90) cc_final: 0.6670 (tpp80) REVERT: A 353 GLU cc_start: 0.6887 (mp0) cc_final: 0.6476 (mp0) REVERT: C 44 PHE cc_start: 0.5949 (t80) cc_final: 0.5623 (t80) REVERT: C 69 LYS cc_start: 0.7509 (ptpt) cc_final: 0.7255 (ptmt) REVERT: C 128 ILE cc_start: 0.7834 (pt) cc_final: 0.7581 (tp) REVERT: C 156 LYS cc_start: 0.6298 (mmtm) cc_final: 0.5973 (mmtm) REVERT: C 452 ASP cc_start: 0.6708 (t0) cc_final: 0.5941 (t0) REVERT: H 21 THR cc_start: 0.7134 (p) cc_final: 0.6837 (p) REVERT: H 68 THR cc_start: 0.8328 (p) cc_final: 0.8123 (p) REVERT: H 93 TYR cc_start: 0.6697 (m-80) cc_final: 0.6407 (m-80) REVERT: L 6 MET cc_start: 0.7315 (ttm) cc_final: 0.6893 (ttm) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.1035 time to fit residues: 26.7174 Evaluate side-chains 112 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 87 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN B 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.101757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.091885 restraints weight = 41365.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.093770 restraints weight = 27329.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.095156 restraints weight = 19498.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.096153 restraints weight = 14704.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.096877 restraints weight = 11606.056| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11641 Z= 0.138 Angle : 0.714 9.476 15815 Z= 0.370 Chirality : 0.046 0.207 1882 Planarity : 0.004 0.054 2008 Dihedral : 6.156 34.125 1574 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.43 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.21), residues: 1457 helix: -0.11 (0.28), residues: 368 sheet: -2.00 (0.34), residues: 196 loop : -2.85 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 105 TYR 0.030 0.002 TYR C 71 PHE 0.011 0.001 PHE H 94 TRP 0.010 0.001 TRP L 37 HIS 0.007 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00311 (11618) covalent geometry : angle 0.70968 (15769) SS BOND : bond 0.00462 ( 23) SS BOND : angle 1.68317 ( 46) hydrogen bonds : bond 0.03840 ( 349) hydrogen bonds : angle 5.08452 ( 948) *********************** 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 163 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.435 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 255 ASP cc_start: 0.6689 (p0) cc_final: 0.6358 (p0) REVERT: C 44 PHE cc_start: 0.5957 (t80) cc_final: 0.5521 (t80) REVERT: C 452 ASP cc_start: 0.6560 (t0) cc_final: 0.5853 (t0) REVERT: H 59 TYR cc_start: 0.6406 (m-10) cc_final: 0.6188 (m-80) REVERT: H 93 TYR cc_start: 0.7049 (m-80) cc_final: 0.6501 (m-80) REVERT: L 90 CYS cc_start: 0.5479 (p) cc_final: 0.3983 (p) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1114 time to fit residues: 25.9430 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 : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 42 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN C 159 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.098941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.088885 restraints weight = 41969.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.090690 restraints weight = 27834.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.092022 restraints weight = 20120.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092971 restraints weight = 15364.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.093681 restraints weight = 12336.980| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.7823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11641 Z= 0.174 Angle : 0.761 8.921 15815 Z= 0.395 Chirality : 0.047 0.209 1882 Planarity : 0.005 0.058 2008 Dihedral : 6.343 33.622 1574 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.60 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.21), residues: 1457 helix: -0.28 (0.27), residues: 367 sheet: -1.62 (0.37), residues: 182 loop : -2.85 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 105 TYR 0.027 0.003 TYR C 71 PHE 0.030 0.002 PHE L 73 TRP 0.014 0.002 TRP L 37 HIS 0.006 0.002 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00404 (11618) covalent geometry : angle 0.75693 (15769) SS BOND : bond 0.00639 ( 23) SS BOND : angle 1.71934 ( 46) hydrogen bonds : bond 0.04306 ( 349) hydrogen bonds : angle 5.20862 ( 948) *********************** 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 159 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.445 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 255 ASP cc_start: 0.6680 (p0) cc_final: 0.6463 (p0) REVERT: B 236 ARG cc_start: 0.6960 (mpp-170) cc_final: 0.6710 (mtt90) REVERT: B 352 MET cc_start: 0.7824 (ttm) cc_final: 0.7438 (ttp) REVERT: C 44 PHE cc_start: 0.5918 (t80) cc_final: 0.5471 (t80) REVERT: C 156 LYS cc_start: 0.6382 (mmtm) cc_final: 0.6068 (mmtm) REVERT: C 348 LEU cc_start: 0.8771 (mt) cc_final: 0.8504 (mt) REVERT: H 59 TYR cc_start: 0.6420 (m-10) cc_final: 0.6108 (m-80) REVERT: H 93 TYR cc_start: 0.7616 (m-80) cc_final: 0.6883 (m-80) REVERT: L 73 PHE cc_start: 0.8076 (m-10) cc_final: 0.7845 (m-10) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1082 time to fit residues: 24.4704 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 : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 122 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 chunk 82 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.100432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.090337 restraints weight = 41441.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.092202 restraints weight = 27388.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.093582 restraints weight = 19642.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.094592 restraints weight = 14954.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095310 restraints weight = 11880.450| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.8212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11641 Z= 0.134 Angle : 0.700 8.101 15815 Z= 0.364 Chirality : 0.046 0.208 1882 Planarity : 0.005 0.052 2008 Dihedral : 6.110 32.273 1574 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.78 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.21), residues: 1457 helix: -0.19 (0.27), residues: 360 sheet: -1.67 (0.35), residues: 197 loop : -2.74 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 105 TYR 0.038 0.002 TYR C 71 PHE 0.013 0.001 PHE A 378 TRP 0.037 0.002 TRP L 37 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00307 (11618) covalent geometry : angle 0.69514 (15769) SS BOND : bond 0.00413 ( 23) SS BOND : angle 1.65161 ( 46) hydrogen bonds : bond 0.03980 ( 349) hydrogen bonds : angle 5.05239 ( 948) *********************** 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 164 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ASP cc_start: 0.6513 (p0) cc_final: 0.6275 (p0) REVERT: B 459 GLU cc_start: 0.7264 (tp30) cc_final: 0.7061 (tp30) REVERT: C 44 PHE cc_start: 0.5974 (t80) cc_final: 0.5462 (t80) REVERT: C 348 LEU cc_start: 0.8821 (mt) cc_final: 0.8517 (mt) REVERT: H 59 TYR cc_start: 0.6571 (m-10) cc_final: 0.6368 (m-80) REVERT: H 93 TYR cc_start: 0.7352 (m-80) cc_final: 0.6907 (m-80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1086 time to fit residues: 25.6301 Evaluate side-chains 102 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.100511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.090457 restraints weight = 41409.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.092271 restraints weight = 27384.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.093624 restraints weight = 19800.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.094602 restraints weight = 15103.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095342 restraints weight = 12064.419| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.8496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11641 Z= 0.133 Angle : 0.716 7.859 15815 Z= 0.370 Chirality : 0.046 0.216 1882 Planarity : 0.004 0.051 2008 Dihedral : 5.983 31.229 1574 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.57 % Favored : 89.36 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.21), residues: 1457 helix: -0.16 (0.27), residues: 369 sheet: -1.51 (0.36), residues: 197 loop : -2.74 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 105 TYR 0.039 0.002 TYR C 71 PHE 0.011 0.001 PHE C 378 TRP 0.026 0.001 TRP L 37 HIS 0.008 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00306 (11618) covalent geometry : angle 0.71149 (15769) SS BOND : bond 0.00322 ( 23) SS BOND : angle 1.70872 ( 46) hydrogen bonds : bond 0.03886 ( 349) hydrogen bonds : angle 4.99713 ( 948) *********************** 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 155 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7005 (m-10) cc_final: 0.6658 (m-10) REVERT: B 352 MET cc_start: 0.8022 (ttm) cc_final: 0.7755 (ttp) REVERT: C 348 LEU cc_start: 0.8817 (mt) cc_final: 0.8589 (mt) REVERT: H 57 THR cc_start: 0.4256 (p) cc_final: 0.3958 (p) REVERT: H 59 TYR cc_start: 0.6566 (m-10) cc_final: 0.6339 (m-80) REVERT: H 93 TYR cc_start: 0.7319 (m-80) cc_final: 0.6788 (m-80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1037 time to fit residues: 23.6715 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 39 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 138 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 43 optimal weight: 0.0270 chunk 68 optimal weight: 5.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.101037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.091008 restraints weight = 41508.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092853 restraints weight = 27770.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.094198 restraints weight = 20075.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095198 restraints weight = 15382.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.095870 restraints weight = 12267.635| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.8779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11641 Z= 0.127 Angle : 0.716 8.738 15815 Z= 0.370 Chirality : 0.046 0.211 1882 Planarity : 0.005 0.058 2008 Dihedral : 5.930 30.249 1574 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.21), residues: 1457 helix: -0.09 (0.27), residues: 369 sheet: -1.63 (0.35), residues: 214 loop : -2.68 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 105 TYR 0.027 0.002 TYR B 254 PHE 0.013 0.001 PHE B 258 TRP 0.021 0.001 TRP L 37 HIS 0.006 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00290 (11618) covalent geometry : angle 0.70830 (15769) SS BOND : bond 0.00388 ( 23) SS BOND : angle 2.02741 ( 46) hydrogen bonds : bond 0.03740 ( 349) hydrogen bonds : angle 4.83998 ( 948) *********************** 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: 0 poor density : 152 time to evaluate : 0.327 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 44 PHE cc_start: 0.6959 (m-10) cc_final: 0.6722 (m-80) REVERT: A 227 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8178 (tmmt) REVERT: B 352 MET cc_start: 0.7967 (ttm) cc_final: 0.7648 (ttp) REVERT: C 348 LEU cc_start: 0.8817 (mt) cc_final: 0.8515 (mt) REVERT: H 57 THR cc_start: 0.4602 (p) cc_final: 0.4265 (p) REVERT: H 93 TYR cc_start: 0.7268 (m-80) cc_final: 0.6896 (m-80) REVERT: L 85 PHE cc_start: 0.7600 (t80) cc_final: 0.7232 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0947 time to fit residues: 21.3160 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 : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 17 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 100 optimal weight: 0.0010 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.098941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088885 restraints weight = 42467.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.090705 restraints weight = 28328.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.092045 restraints weight = 20591.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.093011 restraints weight = 15790.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.093724 restraints weight = 12668.747| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.9126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11641 Z= 0.150 Angle : 0.735 8.504 15815 Z= 0.380 Chirality : 0.047 0.223 1882 Planarity : 0.005 0.058 2008 Dihedral : 5.990 30.795 1574 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.21), residues: 1457 helix: -0.22 (0.27), residues: 373 sheet: -1.66 (0.34), residues: 213 loop : -2.66 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 105 TYR 0.028 0.002 TYR C 71 PHE 0.012 0.001 PHE B 258 TRP 0.018 0.001 TRP L 37 HIS 0.007 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00348 (11618) covalent geometry : angle 0.72796 (15769) SS BOND : bond 0.00467 ( 23) SS BOND : angle 2.07011 ( 46) hydrogen bonds : bond 0.03885 ( 349) hydrogen bonds : angle 4.98520 ( 948) ********************** 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 151 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.325 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 227 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8242 (tmmt) REVERT: C 348 LEU cc_start: 0.8802 (mt) cc_final: 0.8473 (mt) REVERT: C 455 ASP cc_start: 0.7983 (m-30) cc_final: 0.7779 (m-30) REVERT: H 21 THR cc_start: 0.7961 (p) cc_final: 0.7664 (p) REVERT: H 38 ARG cc_start: 0.7349 (ttp80) cc_final: 0.7093 (ttp80) REVERT: L 87 THR cc_start: 0.8593 (m) cc_final: 0.7894 (p) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0920 time to fit residues: 20.3327 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 1 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 43 optimal weight: 0.0000 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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** ** L 92 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 = 0.3810 r_free = 0.3810 target = 0.097656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.087794 restraints weight = 42835.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.089559 restraints weight = 28424.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.090884 restraints weight = 20596.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.091807 restraints weight = 15821.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.092529 restraints weight = 12757.246| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.9599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11641 Z= 0.167 Angle : 0.745 9.119 15815 Z= 0.387 Chirality : 0.047 0.232 1882 Planarity : 0.005 0.062 2008 Dihedral : 6.113 31.759 1574 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.21), residues: 1457 helix: -0.35 (0.27), residues: 378 sheet: -1.39 (0.36), residues: 198 loop : -2.74 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 105 TYR 0.045 0.002 TYR C 71 PHE 0.016 0.002 PHE B 258 TRP 0.018 0.002 TRP L 37 HIS 0.007 0.002 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00391 (11618) covalent geometry : angle 0.73819 (15769) SS BOND : bond 0.00440 ( 23) SS BOND : angle 2.06313 ( 46) hydrogen bonds : bond 0.04040 ( 349) hydrogen bonds : angle 5.11265 ( 948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.05 seconds wall clock time: 30 minutes 14.30 seconds (1814.30 seconds total)