Starting phenix.real_space_refine on Thu Jul 2 16:14:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d6x_30595/07_2026/7d6x_30595.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d6x_30595/07_2026/7d6x_30595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2026/7d6x_30595.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2026/7d6x_30595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2026/7d6x_30595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2026/7d6x_30595.map" model { file = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2026/7d6x_30595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d6x_30595/07_2026/7d6x_30595.cif" } resolution = 2.88 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= 0.000 sd= 0.058 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: 6 Type Number sf(0) Gaussians Fe 11 7.16 5 P 3 5.49 5 S 63 5.16 5 C 5510 2.51 5 N 1527 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8711 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4531 Classifications: {'peptide': 594} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 28, 'TRANS': 565} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1914 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 225} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2141 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'FES': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4955 SG CYS B 54 40.180 50.828 44.564 1.00 47.83 S ATOM 4988 SG CYS B 59 43.330 52.111 45.865 1.00 44.04 S ATOM 5004 SG CYS B 62 40.040 56.787 49.369 1.00 38.59 S ATOM 5095 SG CYS B 74 37.355 54.005 48.548 1.00 44.78 S ATOM 5724 SG CYS B 151 49.821 52.122 59.823 1.00 33.32 S ATOM 5676 SG CYS B 145 48.703 47.346 55.630 1.00 37.11 S ATOM 5699 SG CYS B 148 45.322 53.550 55.841 1.00 34.94 S ATOM 6224 SG CYS B 213 43.207 48.452 59.497 1.00 36.21 S ATOM 6151 SG CYS B 203 52.826 51.709 70.220 1.00 35.58 S ATOM 5754 SG CYS B 155 52.970 56.300 66.188 1.00 35.44 S ATOM 6195 SG CYS B 209 47.472 51.268 66.441 1.00 37.85 S ATOM 8037 SG CYS C 206 48.119 40.050 81.592 1.00 37.27 S ATOM 7292 SG CYS C 114 45.646 46.687 82.164 1.00 36.54 S Time building chain proxies: 1.75, per 1000 atoms: 0.20 Number of scatterers: 8711 At special positions: 0 Unit cell: (84.46, 88.56, 124.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 11 26.01 S 63 16.00 P 3 15.00 O 1597 8.00 N 1527 7.00 C 5510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 191.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 203 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 155 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 209 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 59 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 62 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 74 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 54 " pdb=" FES C 302 " pdb="FE1 FES C 302 " - pdb=" NE2 HIS C 155 " pdb="FE2 FES C 302 " - pdb=" NE2 HIS C 240 " pdb="FE2 FES C 302 " - pdb=" SG CYS C 114 " pdb="FE1 FES C 302 " - pdb=" SG CYS C 206 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 213 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 151 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 148 " Number of angles added : 29 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 46.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 18 through 31 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 66 through 78 Processing helix chain 'A' and resid 83 through 102 Proline residue: A 95 - end of helix removed outlier: 3.617A pdb=" N GLU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 159 removed outlier: 3.705A pdb=" N GLU A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.574A pdb=" N PHE A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 321 through 335 removed outlier: 3.526A pdb=" N ALA A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.979A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 426 through 449 removed outlier: 3.943A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 removed outlier: 3.626A pdb=" N VAL A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.605A pdb=" N GLN A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.835A pdb=" N GLN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 531 through 557 removed outlier: 4.376A pdb=" N ARG A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.550A pdb=" N ILE B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.736A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.099A pdb=" N TYR B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 4.733A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 161 through 165 removed outlier: 3.603A pdb=" N ASN B 164 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.704A pdb=" N ILE B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.775A pdb=" N GLN B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 223 through 236 removed outlier: 3.631A pdb=" N ARG B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 56 removed outlier: 3.688A pdb=" N LEU C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 114 through 125 removed outlier: 3.674A pdb=" N LYS C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 145 Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.803A pdb=" N LEU C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 176 removed outlier: 3.581A pdb=" N PHE C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 160 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 removed outlier: 3.552A pdb=" N ILE C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.823A pdb=" N GLY C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'C' and resid 239 through 264 removed outlier: 3.510A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP C 245 " --> pdb=" O MET C 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.407A pdb=" N GLU A 5 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 201 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS A 7 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 188 " --> pdb=" O THR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169 removed outlier: 6.657A pdb=" N VAL A 34 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE A 169 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 36 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 12 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 205 " --> pdb=" O PHE A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 removed outlier: 5.918A pdb=" N ILE A 394 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 249 removed outlier: 6.444A pdb=" N HIS A 249 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N CYS A 387 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 27 removed outlier: 3.548A pdb=" N ASP B 14 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL B 87 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS B 7 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL B 89 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG B 9 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65 Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.525A pdb=" N TYR C 66 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 178 through 179 336 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: 0.89 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.74: 8823 1.74 - 2.31: 104 2.31 - 2.87: 0 2.87 - 3.44: 0 3.44 - 4.00: 3 Bond restraints: 8930 Sorted by residual: bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 4.001 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 3.925 -1.667 2.00e-02 2.50e+03 6.95e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.729 -1.496 2.00e-02 2.50e+03 5.60e+03 bond pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.296 2.048 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" S2 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.317 2.083 0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 8925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.15: 12083 13.15 - 26.29: 40 26.29 - 39.44: 7 39.44 - 52.59: 0 52.59 - 65.74: 2 Bond angle restraints: 12132 Sorted by residual: angle pdb=" N CYS B 54 " pdb=" CA CYS B 54 " pdb=" C CYS B 54 " ideal model delta sigma weight residual 114.12 148.44 -34.32 1.39e+00 5.18e-01 6.10e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 49.01 65.74 3.00e+00 1.11e-01 4.80e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 50.99 61.60 3.00e+00 1.11e-01 4.22e+02 angle pdb=" N LYS B 58 " pdb=" CA LYS B 58 " pdb=" CB LYS B 58 " ideal model delta sigma weight residual 111.54 83.03 28.51 1.45e+00 4.76e-01 3.87e+02 angle pdb=" S1 FES B 301 " pdb="FE2 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 89.91 14.42 1.14e+00 7.69e-01 1.60e+02 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4708 17.66 - 35.32: 431 35.32 - 52.99: 87 52.99 - 70.65: 16 70.65 - 88.31: 7 Dihedral angle restraints: 5249 sinusoidal: 2107 harmonic: 3142 Sorted by residual: dihedral pdb=" C CYS B 59 " pdb=" N CYS B 59 " pdb=" CA CYS B 59 " pdb=" CB CYS B 59 " ideal model delta harmonic sigma weight residual -122.60 -158.19 35.59 0 2.50e+00 1.60e-01 2.03e+02 dihedral pdb=" N CYS B 59 " pdb=" C CYS B 59 " pdb=" CA CYS B 59 " pdb=" CB CYS B 59 " ideal model delta harmonic sigma weight residual 122.80 158.28 -35.48 0 2.50e+00 1.60e-01 2.01e+02 dihedral pdb=" N LYS B 58 " pdb=" C LYS B 58 " pdb=" CA LYS B 58 " pdb=" CB LYS B 58 " ideal model delta harmonic sigma weight residual 122.80 89.09 33.71 0 2.50e+00 1.60e-01 1.82e+02 ... (remaining 5246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.902: 1316 2.902 - 5.804: 0 5.804 - 8.706: 0 8.706 - 11.607: 0 11.607 - 14.509: 1 Chirality restraints: 1317 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -3.74 14.51 2.00e-01 2.50e+01 5.26e+03 chirality pdb=" CA CYS B 59 " pdb=" N CYS B 59 " pdb=" C CYS B 59 " pdb=" CB CYS B 59 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.89e+01 chirality pdb=" CA LYS B 55 " pdb=" N LYS B 55 " pdb=" C LYS B 55 " pdb=" CB LYS B 55 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.45e+01 ... (remaining 1314 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 606 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 607 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 128 " -0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO C 129 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 145 " 0.017 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C CYS B 145 " -0.062 2.00e-02 2.50e+03 pdb=" O CYS B 145 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE B 146 " 0.020 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 82 2.57 - 3.15: 7006 3.15 - 3.74: 13103 3.74 - 4.32: 20070 4.32 - 4.90: 33391 Nonbonded interactions: 73652 Sorted by model distance: nonbonded pdb=" O2' FAD A 701 " pdb=" O4' FAD A 701 " model vdw 1.988 3.040 nonbonded pdb=" S3 F3S B 303 " pdb="FE3 F3S B 303 " model vdw 2.052 2.688 nonbonded pdb=" S4 F3S B 303 " pdb="FE4 F3S B 303 " model vdw 2.088 2.688 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.130 2.688 nonbonded pdb=" OD1 ASP B 237 " pdb=" OH TYR C 157 " model vdw 2.202 3.040 ... (remaining 73647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.900 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.380 Find NCS groups from input model: 0.050 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 : 0.033 1.701 8946 Z= 1.615 Angle : 1.858 65.736 12161 Z= 0.892 Chirality : 0.412 14.509 1317 Planarity : 0.007 0.112 1560 Dihedral : 14.412 88.310 3239 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.66 % Favored : 88.06 % Rotamer: Outliers : 0.22 % Allowed : 5.11 % Favored : 94.67 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.10 % 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: -2.90 (0.23), residues: 1089 helix: -0.81 (0.24), residues: 425 sheet: -1.32 (0.51), residues: 92 loop : -3.03 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 606 TYR 0.023 0.002 TYR B 202 PHE 0.022 0.002 PHE A 530 TRP 0.010 0.002 TRP C 55 HIS 0.008 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.03166 / 1.57 ( 8930) covalent geometry : angle 1.73503 / 0.89 (12132) hydrogen bonds : bond 0.14905 / 10.10 ( 336) hydrogen bonds : angle 6.22985 / 4.27 ( 948) metal coordination : bond 0.19271 / 11.56 ( 15) metal coordination : angle 13.74231 / 7.74 ( 29) Misc. bond : bond 0.27108 / 14.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.334 Fit side-chains REVERT: A 366 HIS cc_start: 0.7613 (m90) cc_final: 0.7228 (p-80) outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 0.6184 time to fit residues: 74.4812 Evaluate side-chains 79 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 330 ASN A 480 ASN B 133 GLN B 174 HIS B 195 GLN C 88 GLN C 195 ASN C 237 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095429 restraints weight = 12191.635| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.77 r_work: 0.3067 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 8946 Z= 0.174 Angle : 1.533 84.527 12161 Z= 0.453 Chirality : 0.066 1.709 1317 Planarity : 0.006 0.110 1560 Dihedral : 8.550 69.669 1256 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 1.78 % Allowed : 12.11 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.00 % 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: -1.97 (0.25), residues: 1089 helix: 0.26 (0.26), residues: 427 sheet: -1.13 (0.58), residues: 76 loop : -2.67 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.027 0.001 TYR C 121 PHE 0.013 0.001 PHE C 185 TRP 0.012 0.001 TRP B 52 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 8930) covalent geometry : angle 1.08686 / 0.44 (12132) hydrogen bonds : bond 0.04303 / 2.97 ( 336) hydrogen bonds : angle 4.99837 / 3.44 ( 948) metal coordination : bond 0.01194 / 0.67 ( 15) metal coordination : angle 22.17646 / 12.98 ( 29) Misc. bond : bond 0.00191 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.320 Fit side-chains REVERT: A 324 GLU cc_start: 0.6331 (tm-30) cc_final: 0.6115 (tm-30) REVERT: A 366 HIS cc_start: 0.7881 (m90) cc_final: 0.7348 (p-80) REVERT: A 370 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: A 441 LEU cc_start: 0.8254 (tt) cc_final: 0.7768 (tt) REVERT: A 445 ASP cc_start: 0.8230 (m-30) cc_final: 0.7739 (m-30) REVERT: A 603 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8285 (p) REVERT: B 69 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8343 (mmm-85) REVERT: B 211 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8277 (mm-30) outliers start: 16 outliers final: 5 residues processed: 96 average time/residue: 0.4936 time to fit residues: 51.9962 Evaluate side-chains 83 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 211 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.0070 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097340 restraints weight = 12076.100| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.74 r_work: 0.3092 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 8946 Z= 0.155 Angle : 1.428 83.047 12161 Z= 0.428 Chirality : 0.060 1.450 1317 Planarity : 0.006 0.102 1560 Dihedral : 7.734 64.252 1256 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.33 % Allowed : 13.22 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.00 % 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: -1.61 (0.25), residues: 1089 helix: 0.62 (0.27), residues: 440 sheet: -1.26 (0.55), residues: 81 loop : -2.55 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 239 TYR 0.023 0.001 TYR C 121 PHE 0.013 0.001 PHE A 435 TRP 0.012 0.001 TRP C 95 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8930) covalent geometry : angle 1.04320 / 0.42 (12132) hydrogen bonds : bond 0.03803 / 2.61 ( 336) hydrogen bonds : angle 4.75126 / 3.29 ( 948) metal coordination : bond 0.00795 / 0.48 ( 15) metal coordination : angle 20.00544 / 11.33 ( 29) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.488 Fit side-chains REVERT: A 324 GLU cc_start: 0.6385 (tm-30) cc_final: 0.6077 (tm-30) REVERT: A 366 HIS cc_start: 0.7836 (m90) cc_final: 0.7333 (p-80) REVERT: A 441 LEU cc_start: 0.8241 (tt) cc_final: 0.7710 (tt) REVERT: A 445 ASP cc_start: 0.8189 (m-30) cc_final: 0.7740 (m-30) REVERT: A 502 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 572 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5372 (pp-130) REVERT: A 603 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8366 (p) REVERT: B 69 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8434 (mmm-85) REVERT: B 211 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8163 (mm-30) REVERT: C 63 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7331 (p0) REVERT: C 269 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5241 (mp) outliers start: 21 outliers final: 5 residues processed: 99 average time/residue: 0.5069 time to fit residues: 53.6535 Evaluate side-chains 87 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097030 restraints weight = 12804.292| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.79 r_work: 0.3055 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 8946 Z= 0.184 Angle : 1.377 81.587 12161 Z= 0.432 Chirality : 0.061 1.520 1317 Planarity : 0.006 0.094 1560 Dihedral : 7.638 60.677 1256 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 3.00 % Allowed : 14.33 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % 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: -1.41 (0.26), residues: 1089 helix: 0.80 (0.27), residues: 439 sheet: -0.93 (0.53), residues: 97 loop : -2.51 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 239 TYR 0.022 0.001 TYR C 121 PHE 0.014 0.001 PHE A 435 TRP 0.011 0.001 TRP C 95 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 8930) covalent geometry : angle 1.04811 / 0.43 (12132) hydrogen bonds : bond 0.04035 / 2.75 ( 336) hydrogen bonds : angle 4.75324 / 3.29 ( 948) metal coordination : bond 0.01116 / 0.69 ( 15) metal coordination : angle 18.30941 / 10.30 ( 29) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.328 Fit side-chains REVERT: A 324 GLU cc_start: 0.6402 (tm-30) cc_final: 0.6037 (tm-30) REVERT: A 441 LEU cc_start: 0.8272 (tt) cc_final: 0.7778 (tt) REVERT: A 445 ASP cc_start: 0.8210 (m-30) cc_final: 0.7744 (m-30) REVERT: A 502 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 572 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5639 (pp-130) REVERT: A 603 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8376 (p) REVERT: A 612 CYS cc_start: 0.2181 (OUTLIER) cc_final: 0.0351 (m) REVERT: B 31 GLU cc_start: 0.8398 (pt0) cc_final: 0.8149 (pt0) REVERT: B 69 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8415 (mmm-85) REVERT: C 63 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7286 (p0) REVERT: C 259 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7981 (ttm) REVERT: C 269 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5248 (mp) outliers start: 27 outliers final: 11 residues processed: 103 average time/residue: 0.5810 time to fit residues: 63.7845 Evaluate side-chains 91 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095298 restraints weight = 12662.868| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.77 r_work: 0.3031 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 8946 Z= 0.212 Angle : 1.361 80.600 12161 Z= 0.441 Chirality : 0.063 1.571 1317 Planarity : 0.006 0.091 1560 Dihedral : 7.661 56.212 1256 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 3.44 % Allowed : 14.56 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % 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: -1.37 (0.26), residues: 1089 helix: 0.94 (0.27), residues: 426 sheet: -1.00 (0.53), residues: 99 loop : -2.50 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 239 TYR 0.021 0.001 TYR C 121 PHE 0.016 0.002 PHE B 173 TRP 0.011 0.001 TRP C 95 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 ( 8930) covalent geometry : angle 1.05959 / 0.44 (12132) hydrogen bonds : bond 0.04337 / 2.95 ( 336) hydrogen bonds : angle 4.80384 / 3.32 ( 948) metal coordination : bond 0.01345 / 0.81 ( 15) metal coordination : angle 17.52075 / 10.41 ( 29) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.280 Fit side-chains REVERT: A 324 GLU cc_start: 0.6446 (tm-30) cc_final: 0.6042 (tm-30) REVERT: A 445 ASP cc_start: 0.8229 (m-30) cc_final: 0.7750 (m-30) REVERT: A 502 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 572 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6301 (ppp) REVERT: A 603 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8384 (p) REVERT: A 612 CYS cc_start: 0.2192 (OUTLIER) cc_final: 0.0468 (m) REVERT: B 31 GLU cc_start: 0.8402 (pt0) cc_final: 0.8144 (pt0) REVERT: B 69 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8477 (mmm-85) REVERT: C 185 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7777 (t80) REVERT: C 259 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8006 (ttm) REVERT: C 269 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5226 (mp) outliers start: 31 outliers final: 13 residues processed: 101 average time/residue: 0.5495 time to fit residues: 59.0978 Evaluate side-chains 94 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096002 restraints weight = 12274.107| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.77 r_work: 0.3073 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8946 Z= 0.166 Angle : 1.301 80.954 12161 Z= 0.426 Chirality : 0.062 1.568 1317 Planarity : 0.005 0.091 1560 Dihedral : 7.246 51.862 1256 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.89 % Allowed : 15.56 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % 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: -1.28 (0.26), residues: 1089 helix: 0.94 (0.27), residues: 441 sheet: -1.11 (0.56), residues: 81 loop : -2.41 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 239 TYR 0.021 0.001 TYR C 121 PHE 0.013 0.001 PHE C 96 TRP 0.013 0.001 TRP C 95 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 8930) covalent geometry : angle 1.03725 / 0.42 (12132) hydrogen bonds : bond 0.03786 / 2.57 ( 336) hydrogen bonds : angle 4.69396 / 3.24 ( 948) metal coordination : bond 0.00958 / 0.56 ( 15) metal coordination : angle 16.10873 / 9.44 ( 29) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.5459 (tt0) cc_final: 0.4954 (mp0) REVERT: A 324 GLU cc_start: 0.6468 (tm-30) cc_final: 0.6176 (tm-30) REVERT: A 441 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7720 (tt) REVERT: A 445 ASP cc_start: 0.8245 (m-30) cc_final: 0.7789 (m-30) REVERT: A 502 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 572 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6092 (ppp) REVERT: A 603 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 612 CYS cc_start: 0.1807 (OUTLIER) cc_final: 0.0315 (m) REVERT: B 69 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8269 (mmm-85) REVERT: C 63 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7313 (p0) REVERT: C 185 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7623 (t80) REVERT: C 259 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7953 (ttm) REVERT: C 269 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5183 (mp) outliers start: 26 outliers final: 14 residues processed: 101 average time/residue: 0.5330 time to fit residues: 57.6229 Evaluate side-chains 98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 0.0030 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096852 restraints weight = 12315.186| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.81 r_work: 0.3084 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8946 Z= 0.157 Angle : 1.264 81.257 12161 Z= 0.420 Chirality : 0.061 1.557 1317 Planarity : 0.005 0.088 1560 Dihedral : 6.908 50.895 1256 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.00 % Allowed : 16.67 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % 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: -1.12 (0.26), residues: 1089 helix: 1.10 (0.27), residues: 436 sheet: -1.05 (0.57), residues: 81 loop : -2.30 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 239 TYR 0.021 0.001 TYR C 121 PHE 0.013 0.001 PHE A 435 TRP 0.013 0.001 TRP C 95 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 8930) covalent geometry : angle 1.03001 / 0.42 (12132) hydrogen bonds : bond 0.03625 / 2.46 ( 336) hydrogen bonds : angle 4.61578 / 3.19 ( 948) metal coordination : bond 0.00874 / 0.51 ( 15) metal coordination : angle 15.04721 / 8.69 ( 29) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.5420 (tt0) cc_final: 0.4932 (mp0) REVERT: A 324 GLU cc_start: 0.6537 (tm-30) cc_final: 0.6228 (tm-30) REVERT: A 441 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7714 (tt) REVERT: A 445 ASP cc_start: 0.8243 (m-30) cc_final: 0.7798 (m-30) REVERT: A 502 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 572 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.6068 (ppp) REVERT: A 603 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8209 (p) REVERT: A 612 CYS cc_start: 0.1511 (OUTLIER) cc_final: 0.0150 (m) REVERT: B 69 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8264 (mmm-85) REVERT: C 63 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7335 (p0) REVERT: C 185 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7677 (t80) REVERT: C 235 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8482 (mtmp) REVERT: C 259 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7967 (ttm) REVERT: C 269 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5391 (mp) outliers start: 27 outliers final: 12 residues processed: 96 average time/residue: 0.5871 time to fit residues: 60.1741 Evaluate side-chains 96 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 95 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096103 restraints weight = 12197.864| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.79 r_work: 0.3070 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8946 Z= 0.171 Angle : 1.271 81.146 12161 Z= 0.425 Chirality : 0.062 1.561 1317 Planarity : 0.005 0.099 1560 Dihedral : 6.878 50.140 1256 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 3.11 % Allowed : 17.00 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % 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: -1.18 (0.26), residues: 1089 helix: 1.03 (0.27), residues: 441 sheet: -1.05 (0.57), residues: 81 loop : -2.35 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 239 TYR 0.021 0.001 TYR C 121 PHE 0.014 0.001 PHE B 173 TRP 0.012 0.001 TRP C 95 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8930) covalent geometry : angle 1.03825 / 0.42 (12132) hydrogen bonds : bond 0.03789 / 2.57 ( 336) hydrogen bonds : angle 4.63018 / 3.20 ( 948) metal coordination : bond 0.01025 / 0.61 ( 15) metal coordination : angle 15.04062 / 8.77 ( 29) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.5387 (tt0) cc_final: 0.4941 (mp0) REVERT: A 324 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6189 (tm-30) REVERT: A 441 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7731 (tt) REVERT: A 445 ASP cc_start: 0.8246 (m-30) cc_final: 0.7784 (m-30) REVERT: A 502 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 572 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6083 (ppp) REVERT: A 603 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 612 CYS cc_start: 0.1516 (OUTLIER) cc_final: 0.0104 (m) REVERT: B 69 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8264 (mmm-85) REVERT: C 63 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7315 (p0) REVERT: C 185 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7589 (t80) REVERT: C 259 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7943 (ttm) REVERT: C 269 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5171 (mp) outliers start: 28 outliers final: 15 residues processed: 97 average time/residue: 0.5169 time to fit residues: 53.5066 Evaluate side-chains 98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096804 restraints weight = 12149.750| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.78 r_work: 0.3085 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8946 Z= 0.161 Angle : 1.257 81.313 12161 Z= 0.421 Chirality : 0.061 1.554 1317 Planarity : 0.005 0.098 1560 Dihedral : 6.673 49.292 1256 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.00 % Allowed : 17.11 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % 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: -1.14 (0.26), residues: 1089 helix: 1.08 (0.27), residues: 441 sheet: -1.06 (0.57), residues: 81 loop : -2.34 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 239 TYR 0.021 0.001 TYR C 121 PHE 0.013 0.001 PHE C 96 TRP 0.013 0.001 TRP C 95 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 8930) covalent geometry : angle 1.03337 / 0.42 (12132) hydrogen bonds : bond 0.03643 / 2.47 ( 336) hydrogen bonds : angle 4.59954 / 3.17 ( 948) metal coordination : bond 0.00912 / 0.53 ( 15) metal coordination : angle 14.68152 / 8.47 ( 29) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.5308 (tt0) cc_final: 0.4864 (mp0) REVERT: A 324 GLU cc_start: 0.6502 (tm-30) cc_final: 0.6182 (tm-30) REVERT: A 441 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7719 (tt) REVERT: A 445 ASP cc_start: 0.8246 (m-30) cc_final: 0.7786 (m-30) REVERT: A 502 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 572 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.6062 (ppp) REVERT: A 603 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8196 (p) REVERT: A 612 CYS cc_start: 0.1414 (OUTLIER) cc_final: 0.0081 (m) REVERT: B 69 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8268 (mmm-85) REVERT: C 185 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7712 (t80) REVERT: C 259 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7947 (ttm) REVERT: C 269 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5460 (mp) outliers start: 27 outliers final: 16 residues processed: 102 average time/residue: 0.5140 time to fit residues: 56.0367 Evaluate side-chains 99 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097189 restraints weight = 12561.017| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.80 r_work: 0.3062 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8946 Z= 0.180 Angle : 1.276 81.070 12161 Z= 0.430 Chirality : 0.062 1.560 1317 Planarity : 0.005 0.103 1560 Dihedral : 6.766 48.973 1256 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 3.00 % Allowed : 17.22 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % 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: -1.18 (0.26), residues: 1089 helix: 1.03 (0.27), residues: 441 sheet: -1.06 (0.57), residues: 81 loop : -2.36 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 239 TYR 0.021 0.001 TYR C 121 PHE 0.014 0.001 PHE B 173 TRP 0.012 0.001 TRP C 95 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8930) covalent geometry : angle 1.04635 / 0.43 (12132) hydrogen bonds : bond 0.03898 / 2.64 ( 336) hydrogen bonds : angle 4.65146 / 3.21 ( 948) metal coordination : bond 0.01102 / 0.65 ( 15) metal coordination : angle 15.00114 / 8.79 ( 29) Misc. bond : bond 0.00035 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.5380 (tt0) cc_final: 0.4943 (mp0) REVERT: A 324 GLU cc_start: 0.6507 (tm-30) cc_final: 0.6175 (tm-30) REVERT: A 441 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7824 (tt) REVERT: A 445 ASP cc_start: 0.8246 (m-30) cc_final: 0.7816 (m-30) REVERT: A 502 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 572 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6131 (ppp) REVERT: A 603 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8216 (p) REVERT: A 612 CYS cc_start: 0.1552 (OUTLIER) cc_final: 0.0060 (m) REVERT: B 69 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8374 (mmm-85) REVERT: C 185 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7725 (t80) REVERT: C 259 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7959 (ttm) REVERT: C 269 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5191 (mp) outliers start: 27 outliers final: 17 residues processed: 93 average time/residue: 0.5014 time to fit residues: 50.0331 Evaluate side-chains 95 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100631 restraints weight = 12330.969| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.79 r_work: 0.3117 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8946 Z= 0.142 Angle : 1.237 81.594 12161 Z= 0.414 Chirality : 0.061 1.546 1317 Planarity : 0.005 0.102 1560 Dihedral : 6.271 47.467 1256 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.67 % Allowed : 17.67 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % 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: -0.99 (0.26), residues: 1089 helix: 1.22 (0.27), residues: 436 sheet: -1.00 (0.58), residues: 81 loop : -2.24 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 239 TYR 0.021 0.001 TYR C 121 PHE 0.012 0.001 PHE C 96 TRP 0.014 0.001 TRP C 95 HIS 0.002 0.000 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8930) covalent geometry : angle 1.02455 / 0.41 (12132) hydrogen bonds : bond 0.03280 / 2.23 ( 336) hydrogen bonds : angle 4.51423 / 3.11 ( 948) metal coordination : bond 0.00720 / 0.40 ( 15) metal coordination : angle 14.24436 / 7.99 ( 29) Misc. bond : bond 0.00012 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2429.54 seconds wall clock time: 42 minutes 11.15 seconds (2531.15 seconds total)