Starting phenix.real_space_refine on Thu Jul 2 17:01:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d6v_30594/07_2026/7d6v_30594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d6v_30594/07_2026/7d6v_30594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d6v_30594/07_2026/7d6v_30594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d6v_30594/07_2026/7d6v_30594.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d6v_30594/07_2026/7d6v_30594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d6v_30594/07_2026/7d6v_30594.cif" model { file = "/net/cci-nas-00/data/ceres_data/7d6v_30594/07_2026/7d6v_30594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d6v_30594/07_2026/7d6v_30594.cif" } resolution = 2.53 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= -0.001 sd= 0.085 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 5561 2.51 5 N 1541 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 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: 8793 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4601 Classifications: {'peptide': 601} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1910 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 225} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2139 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FES': 1, 'PEV': 1, 'UQ1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5025 SG CYS B 54 43.083 50.586 44.645 1.00 17.96 S ATOM 5054 SG CYS B 59 46.564 51.189 45.166 1.00 16.18 S ATOM 5070 SG CYS B 62 43.079 56.301 48.844 1.00 14.75 S ATOM 5161 SG CYS B 74 40.401 53.492 48.121 1.00 17.98 S ATOM 5790 SG CYS B 151 52.563 51.713 59.294 1.00 11.26 S ATOM 6290 SG CYS B 213 46.003 47.869 59.192 1.00 12.06 S ATOM 5742 SG CYS B 145 51.917 46.652 54.909 1.00 12.48 S ATOM 5765 SG CYS B 148 48.381 52.961 54.895 1.00 11.97 S ATOM 6261 SG CYS B 209 50.606 50.711 65.541 1.00 14.99 S ATOM 6217 SG CYS B 203 56.391 50.847 69.558 1.00 11.63 S ATOM 7358 SG CYS C 114 48.947 46.333 81.743 1.00 10.87 S ATOM 8103 SG CYS C 206 51.468 39.576 81.272 1.00 11.05 S Time building chain proxies: 1.35, per 1000 atoms: 0.15 Number of scatterers: 8793 At special positions: 0 Unit cell: (86.92, 87.74, 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 1614 8.00 N 1541 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS C 132 " distance=2.03 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: 0.92 Conformation dependent library (CDL) restraints added in 265.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 203 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 209 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 155 " 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 303 " pdb="FE2 FES C 303 " - pdb=" SG CYS C 206 " pdb="FE1 FES C 303 " - pdb=" SG CYS C 114 " pdb="FE2 FES C 303 " - pdb=" NE2 HIS C 155 " pdb="FE1 FES C 303 " - pdb=" NE2 HIS C 240 " pdb=" SF4 B 302 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 148 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 151 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 213 " Number of angles added : 29 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 46.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 17 through 31 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 83 through 103 Proline residue: A 95 - end of helix removed outlier: 3.666A pdb=" N GLU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 160 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 321 through 335 removed outlier: 3.801A pdb=" N VAL A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 361 through 373 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: 3.717A pdb=" N SER A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 removed outlier: 3.532A pdb=" N VAL A 461 " --> pdb=" O SER A 457 " (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 519 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: 4.206A pdb=" N ARG A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'B' and resid 32 through 44 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.879A pdb=" N ARG B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.133A pdb=" N TYR B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 5.127A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.640A 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 Processing helix chain 'B' and resid 170 through 182 Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.655A 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 Processing helix chain 'C' and resid 32 through 56 removed outlier: 3.509A pdb=" N LEU C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 4.408A 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 Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.963A pdb=" N LEU C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 176 removed outlier: 3.731A pdb=" N PHE C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.523A pdb=" N GLY C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 222 removed outlier: 3.580A pdb=" N LYS C 222 " --> pdb=" O HIS C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 222' Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'C' and resid 239 through 265 removed outlier: 3.722A pdb=" N TRP C 245 " --> pdb=" O MET C 241 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.326A pdb=" N GLU A 5 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 178 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA A 187 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A 176 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY A 189 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 174 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR A 191 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 172 " --> pdb=" O TYR A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169 removed outlier: 6.517A pdb=" N VAL A 34 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE A 169 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL A 36 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.165A 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: 5.620A 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 253 removed outlier: 6.250A pdb=" N HIS A 249 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N CYS A 387 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 251 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET A 253 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 383 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 500 Processing sheet with id=AA7, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 27 removed outlier: 9.474A pdb=" N VAL B 87 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS B 7 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 65 Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.802A pdb=" N VAL B 102 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 61 363 hydrogen bonds defined for protein. 1035 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: 1.16 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.71: 8905 1.71 - 2.29: 101 2.29 - 2.87: 3 2.87 - 3.45: 0 3.45 - 4.03: 3 Bond restraints: 9012 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 4.027 -1.794 2.00e-02 2.50e+03 8.05e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.879 -1.579 2.00e-02 2.50e+03 6.24e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 3.771 -1.513 2.00e-02 2.50e+03 5.72e+03 bond pdb=" C CYS B 59 " pdb=" N GLY B 60 " ideal model delta sigma weight residual 1.329 1.569 -0.240 1.36e-02 5.41e+03 3.12e+02 bond pdb=" C LYS B 58 " pdb=" N CYS B 59 " ideal model delta sigma weight residual 1.332 1.203 0.129 1.29e-02 6.01e+03 1.00e+02 ... (remaining 9007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.17: 12197 10.17 - 20.34: 33 20.34 - 30.51: 4 30.51 - 40.67: 5 40.67 - 50.84: 2 Bond angle restraints: 12241 Sorted by residual: angle pdb=" N CYS B 59 " pdb=" CA CYS B 59 " pdb=" C CYS B 59 " ideal model delta sigma weight residual 112.93 138.97 -26.04 1.33e+00 5.65e-01 3.83e+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 61.75 50.84 3.00e+00 1.11e-01 2.87e+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 67.94 46.81 3.00e+00 1.11e-01 2.43e+02 angle pdb=" S1 F3S B 303 " pdb="FE3 F3S B 303 " pdb=" S2 F3S B 303 " ideal model delta sigma weight residual 103.25 65.38 37.87 3.00e+00 1.11e-01 1.59e+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 90.00 14.33 1.14e+00 7.69e-01 1.58e+02 ... (remaining 12236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4754 17.66 - 35.32: 438 35.32 - 52.98: 75 52.98 - 70.64: 23 70.64 - 88.30: 9 Dihedral angle restraints: 5299 sinusoidal: 2136 harmonic: 3163 Sorted by residual: 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 122.80 157.98 -35.18 0 2.50e+00 1.60e-01 1.98e+02 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 -156.75 34.15 0 2.50e+00 1.60e-01 1.87e+02 dihedral pdb=" CA SER C 128 " pdb=" C SER C 128 " pdb=" N PRO C 129 " pdb=" CA PRO C 129 " ideal model delta harmonic sigma weight residual 180.00 138.70 41.30 0 5.00e+00 4.00e-02 6.82e+01 ... (remaining 5296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.621: 1323 3.621 - 7.241: 0 7.241 - 10.862: 0 10.862 - 14.482: 0 14.482 - 18.103: 1 Chirality restraints: 1324 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 -7.33 18.10 2.00e-01 2.50e+01 8.19e+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 0.81 1.70 2.00e-01 2.50e+01 7.24e+01 chirality pdb="FE1 SF4 B 302 " pdb=" S2 SF4 B 302 " pdb=" S3 SF4 B 302 " pdb=" S4 SF4 B 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.82 2.00e-01 2.50e+01 1.69e+01 ... (remaining 1321 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 208 " -0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C CYS B 208 " 0.076 2.00e-02 2.50e+03 pdb=" O CYS B 208 " -0.028 2.00e-02 2.50e+03 pdb=" N CYS B 209 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 606 " -0.066 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO A 607 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 128 " -0.051 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO C 129 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.044 5.00e-02 4.00e+02 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 531 2.73 - 3.27: 8610 3.27 - 3.81: 15072 3.81 - 4.36: 19248 4.36 - 4.90: 31856 Nonbonded interactions: 75317 Sorted by model distance: nonbonded pdb=" OD1 ASN A 575 " pdb=" N TRP A 576 " model vdw 2.186 3.120 nonbonded pdb=" OD1 ASP B 237 " pdb=" OH TYR C 157 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP A 73 " pdb=" NH2 ARG A 128 " model vdw 2.210 3.120 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.219 2.688 nonbonded pdb=" NE2 HIS B 161 " pdb=" OE1 GLU C 136 " model vdw 2.242 3.120 ... (remaining 75312 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: 4.960 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 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 : 0.034 1.794 9029 Z= 1.692 Angle : 1.697 50.842 12272 Z= 0.790 Chirality : 0.504 18.103 1324 Planarity : 0.006 0.098 1575 Dihedral : 14.529 88.301 3272 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.58 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.92 (0.25), residues: 1096 helix: 1.04 (0.26), residues: 445 sheet: -0.30 (0.56), residues: 88 loop : -2.15 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 448 TYR 0.018 0.002 TYR C 116 PHE 0.023 0.002 PHE B 173 TRP 0.012 0.001 TRP C 60 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.03116 / 1.56 ( 9012) covalent geometry : angle 1.55869 / 0.79 (12241) SS BOND : bond 0.00333 / 0.18 ( 1) SS BOND : angle 2.33193 / 1.32 ( 2) hydrogen bonds : bond 0.14198 / 9.85 ( 363) hydrogen bonds : angle 6.50891 / 5.18 ( 1035) metal coordination : bond 0.32380 / 17.18 ( 15) metal coordination : angle 13.89255 / 7.12 ( 29) Misc. bond : bond 0.27664 / 14.56 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.239 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.6451 time to fit residues: 83.3994 Evaluate side-chains 102 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 170 HIS A 247 GLN B 195 GLN C 33 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109488 restraints weight = 10083.436| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.20 r_work: 0.3264 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 9029 Z= 0.182 Angle : 1.503 84.138 12272 Z= 0.461 Chirality : 0.059 1.377 1324 Planarity : 0.006 0.091 1575 Dihedral : 8.233 80.186 1269 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.12 % Favored : 90.78 % Rotamer: Outliers : 1.32 % Allowed : 8.17 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.60 (0.26), residues: 1096 helix: 1.50 (0.26), residues: 448 sheet: -0.13 (0.54), residues: 96 loop : -2.20 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 216 TYR 0.025 0.001 TYR C 121 PHE 0.021 0.002 PHE B 173 TRP 0.011 0.001 TRP C 95 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 9012) covalent geometry : angle 1.08379 / 0.45 (12241) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 1.90279 / 1.12 ( 2) hydrogen bonds : bond 0.04955 / 3.42 ( 363) hydrogen bonds : angle 5.40787 / 4.19 ( 1035) metal coordination : bond 0.01695 / 1.05 ( 15) metal coordination : angle 21.44105 / 11.91 ( 29) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.313 Fit side-chains REVERT: A 418 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8326 (ttp) REVERT: B 218 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8748 (mmtp) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 0.5735 time to fit residues: 65.4556 Evaluate side-chains 110 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS A 602 GLN C 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109256 restraints weight = 10229.004| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.21 r_work: 0.3261 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 9029 Z= 0.175 Angle : 1.373 83.450 12272 Z= 0.445 Chirality : 0.059 1.411 1324 Planarity : 0.006 0.080 1575 Dihedral : 7.825 74.999 1269 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.10 % Allowed : 10.38 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.53 (0.26), residues: 1096 helix: 1.66 (0.26), residues: 448 sheet: -0.42 (0.53), residues: 100 loop : -2.20 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 322 TYR 0.023 0.001 TYR C 121 PHE 0.022 0.002 PHE B 173 TRP 0.010 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 9012) covalent geometry : angle 1.05911 / 0.44 (12241) SS BOND : bond 0.00322 / 0.17 ( 1) SS BOND : angle 1.15925 / 0.68 ( 2) hydrogen bonds : bond 0.04655 / 3.21 ( 363) hydrogen bonds : angle 5.22840 / 4.04 ( 1035) metal coordination : bond 0.01146 / 0.64 ( 15) metal coordination : angle 18.01972 / 10.25 ( 29) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.319 Fit side-chains REVERT: B 197 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: B 218 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8733 (mmtp) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 0.5638 time to fit residues: 67.3492 Evaluate side-chains 112 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107627 restraints weight = 10303.097| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.21 r_work: 0.3236 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 9029 Z= 0.196 Angle : 1.378 82.878 12272 Z= 0.452 Chirality : 0.061 1.440 1324 Planarity : 0.006 0.081 1575 Dihedral : 7.816 71.959 1269 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.76 % Allowed : 11.26 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.53 (0.26), residues: 1096 helix: 1.64 (0.26), residues: 448 sheet: -0.42 (0.52), residues: 100 loop : -2.18 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 216 TYR 0.024 0.002 TYR C 116 PHE 0.024 0.002 PHE B 173 TRP 0.009 0.001 TRP C 95 HIS 0.004 0.001 HIS C 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 ( 9012) covalent geometry : angle 1.06721 / 0.45 (12241) SS BOND : bond 0.00428 / 0.23 ( 1) SS BOND : angle 1.11460 / 0.65 ( 2) hydrogen bonds : bond 0.04927 / 3.40 ( 363) hydrogen bonds : angle 5.18587 / 4.00 ( 1035) metal coordination : bond 0.01267 / 0.71 ( 15) metal coordination : angle 17.96312 / 10.54 ( 29) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.216 Fit side-chains REVERT: A 610 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5349 (pp) REVERT: B 197 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7656 (mt-10) outliers start: 25 outliers final: 11 residues processed: 110 average time/residue: 0.5446 time to fit residues: 63.4001 Evaluate side-chains 108 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 455 LYS 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 197 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 81 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS A 602 GLN C 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112660 restraints weight = 10587.608| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.20 r_work: 0.3285 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 9029 Z= 0.156 Angle : 1.339 83.152 12272 Z= 0.429 Chirality : 0.059 1.437 1324 Planarity : 0.005 0.078 1575 Dihedral : 7.418 72.104 1269 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.98 % Allowed : 12.14 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.32 (0.26), residues: 1096 helix: 1.82 (0.26), residues: 448 sheet: -0.36 (0.56), residues: 90 loop : -2.03 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 216 TYR 0.021 0.001 TYR C 121 PHE 0.020 0.002 PHE B 173 TRP 0.009 0.001 TRP B 52 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 9012) covalent geometry : angle 1.03461 / 0.42 (12241) SS BOND : bond 0.00334 / 0.18 ( 1) SS BOND : angle 0.77909 / 0.46 ( 2) hydrogen bonds : bond 0.04158 / 2.86 ( 363) hydrogen bonds : angle 5.06241 / 3.90 ( 1035) metal coordination : bond 0.01029 / 0.55 ( 15) metal coordination : angle 17.50118 / 10.09 ( 29) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.360 Fit side-chains REVERT: A 418 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.7786 (ttt) REVERT: A 610 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5108 (pp) REVERT: B 197 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: C 146 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8012 (mmt-90) outliers start: 27 outliers final: 10 residues processed: 114 average time/residue: 0.5000 time to fit residues: 60.4618 Evaluate side-chains 109 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 496 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 197 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS C 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111030 restraints weight = 10208.562| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.22 r_work: 0.3288 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 9029 Z= 0.154 Angle : 1.332 83.209 12272 Z= 0.426 Chirality : 0.059 1.432 1324 Planarity : 0.005 0.079 1575 Dihedral : 7.215 72.276 1269 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.20 % Allowed : 12.36 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.24 (0.26), residues: 1096 helix: 1.87 (0.26), residues: 448 sheet: -0.34 (0.56), residues: 90 loop : -1.96 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 216 TYR 0.021 0.001 TYR C 121 PHE 0.021 0.002 PHE B 173 TRP 0.010 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9012) covalent geometry : angle 1.03080 / 0.42 (12241) SS BOND : bond 0.00323 / 0.17 ( 1) SS BOND : angle 0.75119 / 0.44 ( 2) hydrogen bonds : bond 0.04122 / 2.83 ( 363) hydrogen bonds : angle 4.99924 / 3.85 ( 1035) metal coordination : bond 0.01020 / 0.55 ( 15) metal coordination : angle 17.38439 / 10.03 ( 29) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 418 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.7765 (ttt) REVERT: A 572 MET cc_start: 0.5070 (mmm) cc_final: 0.4796 (mmt) REVERT: A 610 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5066 (pp) REVERT: B 197 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: C 140 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7551 (mptp) outliers start: 29 outliers final: 12 residues processed: 115 average time/residue: 0.4738 time to fit residues: 57.8895 Evaluate side-chains 111 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 559 GLU 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 197 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS C 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108997 restraints weight = 10565.250| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.21 r_work: 0.3232 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 9029 Z= 0.214 Angle : 1.384 82.842 12272 Z= 0.456 Chirality : 0.061 1.444 1324 Planarity : 0.006 0.078 1575 Dihedral : 7.568 70.077 1269 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.09 % Allowed : 13.36 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.36 (0.26), residues: 1096 helix: 1.71 (0.26), residues: 448 sheet: -0.34 (0.55), residues: 90 loop : -1.99 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 18 TYR 0.025 0.002 TYR C 116 PHE 0.025 0.002 PHE B 173 TRP 0.014 0.001 TRP C 95 HIS 0.004 0.001 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 ( 9012) covalent geometry : angle 1.07283 / 0.45 (12241) SS BOND : bond 0.00348 / 0.18 ( 1) SS BOND : angle 1.04791 / 0.61 ( 2) hydrogen bonds : bond 0.05047 / 3.48 ( 363) hydrogen bonds : angle 5.13973 / 3.97 ( 1035) metal coordination : bond 0.01875 / 1.00 ( 15) metal coordination : angle 18.01002 / 10.67 ( 29) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.206 Fit side-chains REVERT: A 572 MET cc_start: 0.5402 (mmm) cc_final: 0.5085 (mmt) REVERT: A 606 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.4955 (ptt90) REVERT: A 610 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5265 (pp) REVERT: B 197 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: C 140 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7566 (mptp) outliers start: 28 outliers final: 15 residues processed: 110 average time/residue: 0.5466 time to fit residues: 63.6333 Evaluate side-chains 113 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 0.6980 chunk 90 optimal weight: 0.0370 chunk 14 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 104 optimal weight: 0.0060 overall best weight: 0.4474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS C 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112309 restraints weight = 10203.988| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.22 r_work: 0.3305 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 9029 Z= 0.143 Angle : 1.328 83.418 12272 Z= 0.421 Chirality : 0.058 1.427 1324 Planarity : 0.005 0.078 1575 Dihedral : 7.028 71.671 1269 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.98 % Allowed : 13.02 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.15 (0.26), residues: 1096 helix: 1.92 (0.26), residues: 448 sheet: -0.29 (0.56), residues: 90 loop : -1.90 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 216 TYR 0.021 0.001 TYR C 121 PHE 0.019 0.001 PHE B 173 TRP 0.011 0.001 TRP B 52 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9012) covalent geometry : angle 1.02517 / 0.42 (12241) SS BOND : bond 0.00296 / 0.16 ( 1) SS BOND : angle 0.68554 / 0.40 ( 2) hydrogen bonds : bond 0.03864 / 2.65 ( 363) hydrogen bonds : angle 4.96273 / 3.83 ( 1035) metal coordination : bond 0.01163 / 0.60 ( 15) metal coordination : angle 17.38659 / 9.96 ( 29) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 418 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.7800 (ttt) REVERT: A 572 MET cc_start: 0.5096 (mmm) cc_final: 0.4844 (mmt) REVERT: A 610 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.4916 (OUTLIER) REVERT: B 197 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: C 140 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7513 (mptp) REVERT: C 146 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7941 (mmt-90) outliers start: 27 outliers final: 17 residues processed: 114 average time/residue: 0.5426 time to fit residues: 65.5127 Evaluate side-chains 117 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 559 GLU 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 197 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 0.0470 chunk 76 optimal weight: 3.9990 overall best weight: 0.6892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS C 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108416 restraints weight = 10420.192| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.26 r_work: 0.3210 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 9029 Z= 0.160 Angle : 1.341 83.269 12272 Z= 0.431 Chirality : 0.059 1.427 1324 Planarity : 0.006 0.092 1575 Dihedral : 7.023 71.404 1269 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.87 % Allowed : 13.58 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.14 (0.26), residues: 1096 helix: 1.90 (0.26), residues: 448 sheet: -0.23 (0.56), residues: 90 loop : -1.87 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 216 TYR 0.020 0.001 TYR C 121 PHE 0.021 0.002 PHE B 173 TRP 0.014 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 9012) covalent geometry : angle 1.03893 / 0.43 (12241) SS BOND : bond 0.00294 / 0.15 ( 1) SS BOND : angle 0.76793 / 0.45 ( 2) hydrogen bonds : bond 0.04150 / 2.85 ( 363) hydrogen bonds : angle 4.97118 / 3.84 ( 1035) metal coordination : bond 0.01289 / 0.68 ( 15) metal coordination : angle 17.48872 / 10.12 ( 29) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.316 Fit side-chains REVERT: A 418 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.7784 (ttt) REVERT: A 572 MET cc_start: 0.5090 (mmm) cc_final: 0.4811 (mmt) REVERT: A 606 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.4015 (ppt170) REVERT: A 610 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4710 (pp) REVERT: B 197 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: C 140 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7482 (mptp) REVERT: C 146 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8011 (mmt-90) outliers start: 26 outliers final: 15 residues processed: 110 average time/residue: 0.5656 time to fit residues: 65.7176 Evaluate side-chains 119 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 83 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110779 restraints weight = 10485.317| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.27 r_work: 0.3255 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 9029 Z= 0.144 Angle : 1.322 83.442 12272 Z= 0.421 Chirality : 0.058 1.424 1324 Planarity : 0.005 0.092 1575 Dihedral : 6.790 72.377 1269 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.54 % Allowed : 13.69 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.07 (0.26), residues: 1096 helix: 1.95 (0.26), residues: 449 sheet: -0.23 (0.56), residues: 90 loop : -1.81 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 216 TYR 0.021 0.001 TYR C 121 PHE 0.019 0.001 PHE B 173 TRP 0.015 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9012) covalent geometry : angle 1.02619 / 0.42 (12241) SS BOND : bond 0.00296 / 0.16 ( 1) SS BOND : angle 0.64205 / 0.37 ( 2) hydrogen bonds : bond 0.03764 / 2.58 ( 363) hydrogen bonds : angle 4.90880 / 3.79 ( 1035) metal coordination : bond 0.01120 / 0.58 ( 15) metal coordination : angle 17.18726 / 9.83 ( 29) Misc. bond : bond 0.00011 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 418 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7685 (ttt) REVERT: A 572 MET cc_start: 0.4927 (mmm) cc_final: 0.4698 (mmt) REVERT: A 610 LEU cc_start: 0.4981 (OUTLIER) cc_final: 0.4445 (pp) REVERT: B 197 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: C 140 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7478 (mptp) outliers start: 23 outliers final: 12 residues processed: 110 average time/residue: 0.5368 time to fit residues: 62.6246 Evaluate side-chains 107 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS C 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106945 restraints weight = 10470.417| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.27 r_work: 0.3188 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 9029 Z= 0.180 Angle : 1.360 83.191 12272 Z= 0.443 Chirality : 0.060 1.435 1324 Planarity : 0.006 0.098 1575 Dihedral : 7.078 71.390 1269 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.85 % Favored : 91.06 % Rotamer: Outliers : 2.32 % Allowed : 14.46 % Favored : 83.22 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 3.64 % 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: -0.15 (0.26), residues: 1096 helix: 1.85 (0.26), residues: 448 sheet: -0.18 (0.56), residues: 90 loop : -1.84 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 216 TYR 0.022 0.001 TYR C 116 PHE 0.023 0.002 PHE B 173 TRP 0.012 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 9012) covalent geometry : angle 1.05618 / 0.44 (12241) SS BOND : bond 0.00328 / 0.17 ( 1) SS BOND : angle 0.86850 / 0.51 ( 2) hydrogen bonds : bond 0.04511 / 3.10 ( 363) hydrogen bonds : angle 5.01311 / 3.87 ( 1035) metal coordination : bond 0.01422 / 0.77 ( 15) metal coordination : angle 17.64839 / 10.30 ( 29) Misc. bond : bond 0.00044 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.06 seconds wall clock time: 44 minutes 25.49 seconds (2665.49 seconds total)