Starting phenix.real_space_refine on Tue Mar 3 23:58:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d6v_30594/03_2026/7d6v_30594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d6v_30594/03_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_30594/03_2026/7d6v_30594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d6v_30594/03_2026/7d6v_30594.map" model { file = "/net/cci-nas-00/data/ceres_data/7d6v_30594/03_2026/7d6v_30594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d6v_30594/03_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-5986/lib/python3.9/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: 1.84, per 1000 atoms: 0.21 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: 0.52 Conformation dependent library (CDL) restraints added in 253.2 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: 0.19 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: 1.36 Time building geometry restraints manager: 0.67 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 - 28.95: 5138 28.95 - 57.89: 189 57.89 - 86.83: 24 86.83 - 115.78: 1 115.78 - 144.72: 1 Dihedral angle restraints: 5353 sinusoidal: 2190 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 5350 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: 0.010 Normalize map: mean=0, sd=1: 5.340 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.840 Find NCS groups from input model: 0.040 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:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 14.912 144.725 3326 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 covalent geometry : bond 0.03116 ( 9012) covalent geometry : angle 1.55869 (12241) SS BOND : bond 0.00333 ( 1) SS BOND : angle 2.33193 ( 2) hydrogen bonds : bond 0.14198 ( 363) hydrogen bonds : angle 6.50891 ( 1035) metal coordination : bond 0.32380 ( 15) metal coordination : angle 13.89255 ( 29) Misc. bond : bond 0.27664 ( 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 : 0.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.7843 time to fit residues: 101.2931 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 : 0.330 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.125938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109483 restraints weight = 10103.296| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.20 r_work: 0.3261 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0915 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= 0.182 Angle : 1.518 85.556 12272 Z= 0.462 Chirality : 0.059 1.371 1324 Planarity : 0.006 0.091 1575 Dihedral : 10.032 141.070 1323 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.03 % Favored : 90.88 % 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: -0.58 (0.26), residues: 1096 helix: 1.51 (0.26), residues: 448 sheet: -0.29 (0.56), residues: 88 loop : -2.12 (0.24), residues: 560 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 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9012) covalent geometry : angle 1.08685 (12241) SS BOND : bond 0.00039 ( 1) SS BOND : angle 1.94862 ( 2) hydrogen bonds : bond 0.04976 ( 363) hydrogen bonds : angle 5.41377 ( 1035) metal coordination : bond 0.01612 ( 15) metal coordination : angle 21.83504 ( 29) Misc. bond : bond 0.00053 ( 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 115 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.362 Fit side-chains REVERT: A 418 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8332 (ttp) REVERT: B 218 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8748 (mmtp) REVERT: C 33 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8750 (tt0) outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 0.6729 time to fit residues: 74.6046 Evaluate side-chains 110 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 33 GLN 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: 0.7980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 602 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109668 restraints weight = 10092.243| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.20 r_work: 0.3265 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 9029 Z= 0.171 Angle : 1.421 82.941 12272 Z= 0.443 Chirality : 0.060 1.433 1324 Planarity : 0.006 0.080 1575 Dihedral : 9.598 140.921 1323 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.10 % Allowed : 9.93 % Favored : 87.97 % 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: -0.41 (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 0.021 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 covalent geometry : bond 0.00382 ( 9012) covalent geometry : angle 1.05197 (12241) SS BOND : bond 0.00265 ( 1) SS BOND : angle 1.18879 ( 2) hydrogen bonds : bond 0.04581 ( 363) hydrogen bonds : angle 5.23202 ( 1035) metal coordination : bond 0.01119 ( 15) metal coordination : angle 19.68510 ( 29) Misc. bond : bond 0.00065 ( 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 : 0.434 Fit side-chains REVERT: B 197 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: B 218 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8748 (mmtp) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 0.6989 time to fit residues: 83.5240 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 : 0.413 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3522 r_free = 0.3522 target = 0.126109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109625 restraints weight = 10280.433| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.22 r_work: 0.3262 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1237 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= 0.168 Angle : 1.355 82.973 12272 Z= 0.437 Chirality : 0.060 1.432 1324 Planarity : 0.006 0.081 1575 Dihedral : 9.427 140.379 1323 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % 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: -0.45 (0.26), residues: 1096 helix: 1.73 (0.26), residues: 448 sheet: -0.42 (0.52), residues: 100 loop : -2.16 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 216 TYR 0.022 0.001 TYR C 121 PHE 0.022 0.002 PHE B 173 TRP 0.009 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9012) covalent geometry : angle 1.04639 (12241) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.94565 ( 2) hydrogen bonds : bond 0.04468 ( 363) hydrogen bonds : angle 5.13281 ( 1035) metal coordination : bond 0.01119 ( 15) metal coordination : angle 17.74791 ( 29) Misc. bond : bond 0.00028 ( 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 126 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.349 Fit side-chains REVERT: A 610 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5277 (pp) REVERT: B 197 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7659 (mt-10) outliers start: 25 outliers final: 10 residues processed: 110 average time/residue: 0.7467 time to fit residues: 86.6980 Evaluate side-chains 109 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 441 LEU 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 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: 0.6980 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3517 r_free = 0.3517 target = 0.125887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109441 restraints weight = 10237.992| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.21 r_work: 0.3262 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1331 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= 0.170 Angle : 1.351 83.076 12272 Z= 0.436 Chirality : 0.060 1.438 1324 Planarity : 0.006 0.078 1575 Dihedral : 9.328 139.943 1323 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.76 % Allowed : 12.36 % 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: -0.35 (0.26), residues: 1096 helix: 1.77 (0.26), residues: 448 sheet: -0.37 (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 0.022 0.001 TYR C 116 PHE 0.022 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 covalent geometry : bond 0.00382 ( 9012) covalent geometry : angle 1.04514 (12241) SS BOND : bond 0.00374 ( 1) SS BOND : angle 0.90416 ( 2) hydrogen bonds : bond 0.04466 ( 363) hydrogen bonds : angle 5.09965 ( 1035) metal coordination : bond 0.01129 ( 15) metal coordination : angle 17.65125 ( 29) Misc. bond : bond 0.00037 ( 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 126 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.365 Fit side-chains REVERT: A 418 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.7894 (ttt) REVERT: A 572 MET cc_start: 0.5243 (mmm) cc_final: 0.4968 (mmt) REVERT: A 610 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5274 (pp) REVERT: B 141 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: B 197 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7678 (mt-10) outliers start: 25 outliers final: 9 residues processed: 113 average time/residue: 0.7138 time to fit residues: 85.2199 Evaluate side-chains 110 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 141 GLU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 205 ILE 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=3.00 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110024 restraints weight = 10194.200| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.21 r_work: 0.3275 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1408 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= 0.164 Angle : 1.345 83.186 12272 Z= 0.433 Chirality : 0.059 1.427 1324 Planarity : 0.005 0.081 1575 Dihedral : 9.199 139.299 1323 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.65 % Allowed : 12.69 % Favored : 84.66 % 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: -0.30 (0.26), residues: 1096 helix: 1.81 (0.26), residues: 448 sheet: -0.33 (0.56), residues: 90 loop : -2.00 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 216 TYR 0.020 0.001 TYR C 116 PHE 0.021 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 covalent geometry : bond 0.00366 ( 9012) covalent geometry : angle 1.04070 (12241) SS BOND : bond 0.00348 ( 1) SS BOND : angle 0.84525 ( 2) hydrogen bonds : bond 0.04337 ( 363) hydrogen bonds : angle 5.06293 ( 1035) metal coordination : bond 0.01111 ( 15) metal coordination : angle 17.56403 ( 29) Misc. bond : bond 0.00027 ( 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 122 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.277 Fit side-chains REVERT: A 418 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.7835 (ttt) REVERT: A 572 MET cc_start: 0.5208 (mmm) cc_final: 0.4920 (mmt) REVERT: A 610 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5067 (pp) REVERT: B 141 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: B 197 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7676 (mt-10) outliers start: 24 outliers final: 10 residues processed: 113 average time/residue: 0.7018 time to fit residues: 83.8465 Evaluate side-chains 112 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 441 LEU 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 141 GLU 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 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: 0.7980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 37 optimal weight: 0.0570 chunk 102 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.124892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108423 restraints weight = 10238.178| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.21 r_work: 0.3248 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 9029 Z= 0.187 Angle : 1.366 83.082 12272 Z= 0.445 Chirality : 0.060 1.431 1324 Planarity : 0.006 0.079 1575 Dihedral : 9.222 139.785 1323 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.20 % Allowed : 12.69 % Favored : 84.11 % 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: -0.34 (0.26), residues: 1096 helix: 1.75 (0.26), residues: 448 sheet: -0.33 (0.55), residues: 90 loop : -1.99 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 216 TYR 0.023 0.002 TYR C 116 PHE 0.024 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 covalent geometry : bond 0.00425 ( 9012) covalent geometry : angle 1.05836 (12241) SS BOND : bond 0.00348 ( 1) SS BOND : angle 0.93913 ( 2) hydrogen bonds : bond 0.04711 ( 363) hydrogen bonds : angle 5.10332 ( 1035) metal coordination : bond 0.01504 ( 15) metal coordination : angle 17.78872 ( 29) Misc. bond : bond 0.00045 ( 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 125 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.370 Fit side-chains REVERT: A 572 MET cc_start: 0.5271 (mmm) cc_final: 0.4975 (mmt) REVERT: A 610 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5202 (pp) REVERT: B 141 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: B 197 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: C 140 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7559 (mptp) outliers start: 29 outliers final: 13 residues processed: 111 average time/residue: 0.6705 time to fit residues: 78.7324 Evaluate side-chains 111 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 431 ASP Chi-restraints excluded: chain A residue 455 LYS 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 141 GLU 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 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: 0.0010 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3561 r_free = 0.3561 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112748 restraints weight = 10214.749| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.22 r_work: 0.3312 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1622 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 : 1.327 83.477 12272 Z= 0.421 Chirality : 0.058 1.422 1324 Planarity : 0.005 0.080 1575 Dihedral : 8.664 137.182 1323 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.76 % Allowed : 12.80 % 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: -0.15 (0.26), residues: 1096 helix: 1.93 (0.26), residues: 449 sheet: -0.25 (0.56), residues: 90 loop : -1.91 (0.25), residues: 557 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 0.014 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9012) covalent geometry : angle 1.02599 (12241) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.61461 ( 2) hydrogen bonds : bond 0.03824 ( 363) hydrogen bonds : angle 4.95618 ( 1035) metal coordination : bond 0.01174 ( 15) metal coordination : angle 17.33388 ( 29) Misc. bond : bond 0.00012 ( 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 130 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8101 (m-30) cc_final: 0.7873 (m-30) REVERT: A 418 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7780 (ttt) REVERT: A 572 MET cc_start: 0.5005 (mmm) cc_final: 0.4767 (mmt) REVERT: A 610 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.4808 (OUTLIER) REVERT: B 141 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: B 197 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: C 140 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7498 (mptp) outliers start: 25 outliers final: 11 residues processed: 115 average time/residue: 0.7041 time to fit residues: 85.4461 Evaluate side-chains 111 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 141 GLU 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 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: 0.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111084 restraints weight = 10444.545| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.20 r_work: 0.3268 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 9029 Z= 0.179 Angle : 1.358 83.225 12272 Z= 0.441 Chirality : 0.060 1.426 1324 Planarity : 0.006 0.090 1575 Dihedral : 8.631 138.322 1323 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.32 % Allowed : 13.91 % 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: -0.19 (0.26), residues: 1096 helix: 1.86 (0.26), residues: 448 sheet: -0.18 (0.56), residues: 90 loop : -1.91 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 17 TYR 0.022 0.001 TYR C 116 PHE 0.023 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 covalent geometry : bond 0.00404 ( 9012) covalent geometry : angle 1.05368 (12241) SS BOND : bond 0.00337 ( 1) SS BOND : angle 0.87419 ( 2) hydrogen bonds : bond 0.04494 ( 363) hydrogen bonds : angle 5.02390 ( 1035) metal coordination : bond 0.01446 ( 15) metal coordination : angle 17.64123 ( 29) Misc. bond : bond 0.00041 ( 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 120 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 418 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.7866 (ttt) REVERT: A 572 MET cc_start: 0.5173 (mmm) cc_final: 0.4901 (mmt) REVERT: A 606 ARG cc_start: 0.5859 (OUTLIER) cc_final: 0.3949 (ppt170) REVERT: A 610 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.4862 (pp) REVERT: B 141 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: B 197 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: C 140 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7560 (mptp) outliers start: 21 outliers final: 11 residues processed: 111 average time/residue: 0.6940 time to fit residues: 81.4677 Evaluate side-chains 112 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 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 141 GLU 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 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 72 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 247 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 = 0.3546 r_free = 0.3546 target = 0.129175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112164 restraints weight = 10443.939| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.27 r_work: 0.3279 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1813 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= 0.139 Angle : 1.318 83.546 12272 Z= 0.418 Chirality : 0.058 1.418 1324 Planarity : 0.005 0.091 1575 Dihedral : 7.944 135.177 1323 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.21 % Allowed : 14.02 % 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: -0.01 (0.27), residues: 1096 helix: 2.02 (0.26), residues: 446 sheet: -0.18 (0.57), residues: 90 loop : -1.79 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 216 TYR 0.022 0.001 TYR C 121 PHE 0.019 0.001 PHE B 173 TRP 0.016 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9012) covalent geometry : angle 1.02392 (12241) SS BOND : bond 0.00296 ( 1) SS BOND : angle 0.61756 ( 2) hydrogen bonds : bond 0.03590 ( 363) hydrogen bonds : angle 4.88693 ( 1035) metal coordination : bond 0.01011 ( 15) metal coordination : angle 17.11393 ( 29) Misc. bond : bond 0.00024 ( 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 116 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 572 MET cc_start: 0.5034 (mmm) cc_final: 0.4821 (mmt) REVERT: B 141 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: C 140 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7467 (mptp) outliers start: 20 outliers final: 9 residues processed: 107 average time/residue: 0.7005 time to fit residues: 79.2769 Evaluate side-chains 105 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 218 LYS 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: 0.5980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 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: 0.0980 chunk 101 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3491 r_free = 0.3491 target = 0.124875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107812 restraints weight = 10437.276| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.27 r_work: 0.3192 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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= 0.172 Angle : 1.351 83.290 12272 Z= 0.438 Chirality : 0.060 1.420 1324 Planarity : 0.006 0.098 1575 Dihedral : 8.139 136.279 1323 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.03 % Favored : 90.88 % Rotamer: Outliers : 1.88 % Allowed : 14.68 % Favored : 83.44 % Cbeta Deviations : 0.10 % 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: -0.10 (0.26), residues: 1096 helix: 1.92 (0.26), residues: 448 sheet: -0.13 (0.57), residues: 90 loop : -1.85 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 216 TYR 0.021 0.001 TYR C 116 PHE 0.022 0.002 PHE B 173 TRP 0.013 0.001 TRP C 95 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9012) covalent geometry : angle 1.04994 (12241) SS BOND : bond 0.00306 ( 1) SS BOND : angle 0.82581 ( 2) hydrogen bonds : bond 0.04348 ( 363) hydrogen bonds : angle 4.97637 ( 1035) metal coordination : bond 0.01380 ( 15) metal coordination : angle 17.53463 ( 29) Misc. bond : bond 0.00050 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3042.16 seconds wall clock time: 52 minutes 28.54 seconds (3148.54 seconds total)