Starting phenix.real_space_refine on Fri Jul 3 08:06:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ozs_13134/07_2026/7ozs_13134.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozs_13134/07_2026/7ozs_13134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2026/7ozs_13134.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2026/7ozs_13134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2026/7ozs_13134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2026/7ozs_13134.map" model { file = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2026/7ozs_13134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2026/7ozs_13134.cif" } resolution = 3.5 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= 0.013 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 102 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 119 5.49 5 S 38 5.16 5 C 7615 2.51 5 N 2272 2.21 5 O 2726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 12770 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1147 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 3 Chain: "A" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2166 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 268} Chain breaks: 3 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 641 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 74} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1901 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "3" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2536 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 54} Link IDs: {'rna2p': 10, 'rna3p': 108} Chain: "E" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4264 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 544} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 79 Time building chain proxies: 2.16, per 1000 atoms: 0.17 Number of scatterers: 12770 At special positions: 0 Unit cell: (88.956, 119.667, 146.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 119 15.00 O 2726 8.00 N 2272 7.00 C 7615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 382.5 milliseconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 58.3% alpha, 8.8% beta 33 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.762A pdb=" N GLU B 12 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.737A pdb=" N LYS B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 88 removed outlier: 4.171A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.788A pdb=" N VAL B 139 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 168 removed outlier: 3.813A pdb=" N PHE B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 94 through 113 Processing helix chain 'A' and resid 160 through 173 removed outlier: 3.697A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.605A pdb=" N TYR A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 235 through 253 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 283 through 298 Processing helix chain 'D' and resid 43 through 69 removed outlier: 4.058A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 39 through 53 Processing helix chain 'C' and resid 72 through 83 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.538A pdb=" N GLN C 128 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 129 " --> pdb=" O ILE C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 155 through 169 removed outlier: 4.014A pdb=" N ASP C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'E' and resid 9 through 17 removed outlier: 4.049A pdb=" N UNK E 15 " --> pdb=" O UNK E 12 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N UNK E 17 " --> pdb=" O UNK E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 47 through 64 removed outlier: 3.988A pdb=" N GLY F 56 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA F 57 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 74 Processing helix chain 'F' and resid 75 through 83 Processing helix chain 'F' and resid 89 through 107 removed outlier: 3.598A pdb=" N ARG F 93 " --> pdb=" O ASN F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 118 removed outlier: 3.898A pdb=" N CYS F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 137 removed outlier: 4.171A pdb=" N ALA F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 169 Processing helix chain 'F' and resid 171 through 181 removed outlier: 3.577A pdb=" N LYS F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 195 removed outlier: 4.056A pdb=" N LEU F 185 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 213 Processing helix chain 'F' and resid 216 through 225 Processing helix chain 'F' and resid 230 through 241 Processing helix chain 'F' and resid 245 through 260 removed outlier: 3.957A pdb=" N ALA F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL F 252 " --> pdb=" O MET F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 288 removed outlier: 3.873A pdb=" N LEU F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 329 removed outlier: 4.391A pdb=" N GLN F 320 " --> pdb=" O GLY F 316 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU F 321 " --> pdb=" O THR F 317 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 399 Processing helix chain 'F' and resid 411 through 420 Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 435 through 458 Processing helix chain 'F' and resid 461 through 465 removed outlier: 3.777A pdb=" N GLY F 464 " --> pdb=" O PHE F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 484 Proline residue: F 475 - end of helix Processing helix chain 'F' and resid 484 through 491 removed outlier: 3.647A pdb=" N ALA F 491 " --> pdb=" O PRO F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 514 removed outlier: 3.874A pdb=" N VAL F 512 " --> pdb=" O ALA F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 535 removed outlier: 3.682A pdb=" N LYS F 526 " --> pdb=" O ASN F 522 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS F 535 " --> pdb=" O TYR F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 553 removed outlier: 3.780A pdb=" N GLN F 553 " --> pdb=" O ASP F 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 550 through 553' Processing helix chain 'F' and resid 554 through 567 removed outlier: 3.578A pdb=" N LYS F 558 " --> pdb=" O GLY F 554 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 589 removed outlier: 3.511A pdb=" N ASN F 576 " --> pdb=" O PRO F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 609 Processing helix chain 'F' and resid 614 through 620 removed outlier: 4.171A pdb=" N LYS F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 644 removed outlier: 3.912A pdb=" N HIS F 629 " --> pdb=" O GLY F 625 " (cutoff:3.500A) Proline residue: F 635 - end of helix Processing helix chain 'F' and resid 649 through 674 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48 removed outlier: 6.936A pdb=" N CYS B 131 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 18 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B 129 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU B 20 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP B 127 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 93 removed outlier: 6.983A pdb=" N LEU B 92 " --> pdb=" O ARG B 173 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 67 Processing sheet with id=AA6, first strand: chain 'D' and resid 22 through 24 removed outlier: 6.705A pdb=" N MET C 141 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL C 187 " --> pdb=" O MET C 141 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 143 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ALA C 189 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA C 145 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU C 225 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET C 253 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 227 " --> pdb=" O PRO C 251 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 229 " --> pdb=" O HIS C 249 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU C 115 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N MET C 260 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET C 113 " --> pdb=" O MET C 260 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE C 106 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU C 31 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY C 90 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU C 33 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 72 557 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2952 1.33 - 1.45: 3202 1.45 - 1.57: 6794 1.57 - 1.69: 238 1.69 - 1.81: 61 Bond restraints: 13247 Sorted by residual: bond pdb=" CA GLY D 78 " pdb=" C GLY D 78 " ideal model delta sigma weight residual 1.520 1.504 0.016 7.30e-03 1.88e+04 4.84e+00 bond pdb=" CA ALA F 571 " pdb=" CB ALA F 571 " ideal model delta sigma weight residual 1.537 1.508 0.030 1.47e-02 4.63e+03 4.04e+00 bond pdb=" CB GLN B 166 " pdb=" CG GLN B 166 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" CB LYS B 86 " pdb=" CG LYS B 86 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.61e+00 bond pdb=" CA ASP F 550 " pdb=" C ASP F 550 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.53e+00 ... (remaining 13242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 18247 2.77 - 5.54: 223 5.54 - 8.30: 37 8.30 - 11.07: 9 11.07 - 13.84: 2 Bond angle restraints: 18518 Sorted by residual: angle pdb=" N ALA F 571 " pdb=" CA ALA F 571 " pdb=" C ALA F 571 " ideal model delta sigma weight residual 108.22 99.47 8.75 9.00e-01 1.23e+00 9.45e+01 angle pdb=" C PRO F 140 " pdb=" N PRO F 141 " pdb=" CA PRO F 141 " ideal model delta sigma weight residual 127.00 140.84 -13.84 2.40e+00 1.74e-01 3.33e+01 angle pdb=" C ASP F 569 " pdb=" N PRO F 570 " pdb=" CA PRO F 570 " ideal model delta sigma weight residual 119.83 113.63 6.20 1.08e+00 8.57e-01 3.29e+01 angle pdb=" C PRO F 140 " pdb=" N PRO F 141 " pdb=" CD PRO F 141 " ideal model delta sigma weight residual 120.60 109.00 11.60 2.20e+00 2.07e-01 2.78e+01 angle pdb=" CB LYS B 86 " pdb=" CG LYS B 86 " pdb=" CD LYS B 86 " ideal model delta sigma weight residual 111.30 121.52 -10.22 2.30e+00 1.89e-01 1.98e+01 ... (remaining 18513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.80: 7554 31.80 - 63.61: 201 63.61 - 95.41: 17 95.41 - 127.21: 2 127.21 - 159.02: 1 Dihedral angle restraints: 7775 sinusoidal: 3884 harmonic: 3891 Sorted by residual: dihedral pdb=" CA ASN A 70 " pdb=" C ASN A 70 " pdb=" N GLY A 71 " pdb=" CA GLY A 71 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR A 56 " pdb=" C THR A 56 " pdb=" N ASN A 57 " pdb=" CA ASN A 57 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C4' G 3 52 " pdb=" C3' G 3 52 " pdb=" O3' G 3 52 " pdb=" P U 3 53 " ideal model delta sinusoidal sigma weight residual 220.00 60.98 159.02 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 7772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1943 0.065 - 0.129: 246 0.129 - 0.194: 30 0.194 - 0.259: 6 0.259 - 0.324: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C3' G 3 52 " pdb=" C4' G 3 52 " pdb=" O3' G 3 52 " pdb=" C2' G 3 52 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA LEU F 566 " pdb=" N LEU F 566 " pdb=" C LEU F 566 " pdb=" CB LEU F 566 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE B 15 " pdb=" CA ILE B 15 " pdb=" CG1 ILE B 15 " pdb=" CG2 ILE B 15 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2227 not shown) Planarity restraints: 1937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 563 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C VAL F 563 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL F 563 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY F 564 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 569 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO F 570 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 570 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 570 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 134 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO C 135 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 135 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 135 " 0.033 5.00e-02 4.00e+02 ... (remaining 1934 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3340 2.81 - 3.33: 11346 3.33 - 3.85: 22371 3.85 - 4.38: 25127 4.38 - 4.90: 40074 Nonbonded interactions: 102258 Sorted by model distance: nonbonded pdb=" O LEU F 132 " pdb=" OG1 THR F 136 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR A 62 " pdb=" O ALA A 78 " model vdw 2.311 3.040 nonbonded pdb=" O2' G 3 76 " pdb=" O6 G 3 100 " model vdw 2.316 3.040 nonbonded pdb=" OD2 ASP C 48 " pdb=" OH TYR C 123 " model vdw 2.323 3.040 nonbonded pdb=" O GLU F 416 " pdb=" OG1 THR F 420 " model vdw 2.325 3.040 ... (remaining 102253 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.004 0.056 13247 Z= 0.199 Angle : 0.795 13.842 18518 Z= 0.426 Chirality : 0.046 0.324 2230 Planarity : 0.006 0.073 1937 Dihedral : 13.794 159.017 5239 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.29 % Allowed : 0.87 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1282 helix: -0.69 (0.17), residues: 688 sheet: -0.10 (0.47), residues: 131 loop : -1.41 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 173 TYR 0.018 0.001 TYR A 201 PHE 0.015 0.002 PHE A 163 TRP 0.015 0.002 TRP F 154 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (13247) covalent geometry : angle 0.79451 / 0.43 (18518) hydrogen bonds : bond 0.17479 / 11.54 ( 640) hydrogen bonds : angle 6.62450 / 4.54 ( 1760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: D 48 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7921 (tp30) REVERT: D 79 VAL cc_start: 0.8810 (t) cc_final: 0.8425 (p) outliers start: 3 outliers final: 1 residues processed: 85 average time/residue: 0.0833 time to fit residues: 11.3913 Evaluate side-chains 58 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 63 GLN C 93 ASN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.058460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.041492 restraints weight = 56964.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.043106 restraints weight = 27434.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.044109 restraints weight = 18279.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044667 restraints weight = 14472.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.045081 restraints weight = 12651.763| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 13247 Z= 0.381 Angle : 0.723 7.255 18518 Z= 0.374 Chirality : 0.043 0.243 2230 Planarity : 0.005 0.052 1937 Dihedral : 10.914 174.752 2867 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.15 % Allowed : 8.17 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.23), residues: 1282 helix: 1.24 (0.20), residues: 698 sheet: -0.19 (0.45), residues: 136 loop : -1.11 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 182 TYR 0.024 0.002 TYR A 201 PHE 0.022 0.002 PHE C 149 TRP 0.013 0.002 TRP A 95 HIS 0.008 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.38 (13247) covalent geometry : angle 0.72294 / 0.37 (18518) hydrogen bonds : bond 0.04743 / 3.14 ( 640) hydrogen bonds : angle 4.47665 / 3.09 ( 1760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.398 Fit side-chains REVERT: A 166 MET cc_start: 0.8654 (tmm) cc_final: 0.8336 (tmm) REVERT: D 48 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8310 (tp30) REVERT: D 93 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6857 (tm-30) REVERT: D 94 LYS cc_start: 0.8722 (mttp) cc_final: 0.8452 (mptt) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 0.0860 time to fit residues: 9.3240 Evaluate side-chains 62 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain F residue 637 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 5 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 chunk 90 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.059771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.042895 restraints weight = 56452.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044623 restraints weight = 25564.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045688 restraints weight = 16479.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046355 restraints weight = 12793.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046693 restraints weight = 11012.957| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13247 Z= 0.149 Angle : 0.537 6.770 18518 Z= 0.277 Chirality : 0.037 0.209 2230 Planarity : 0.004 0.052 1937 Dihedral : 10.751 173.660 2864 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.15 % Allowed : 9.52 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1282 helix: 1.80 (0.20), residues: 700 sheet: -0.01 (0.45), residues: 135 loop : -0.95 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 68 TYR 0.016 0.001 TYR A 201 PHE 0.010 0.001 PHE A 163 TRP 0.012 0.001 TRP F 97 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (13247) covalent geometry : angle 0.53663 / 0.28 (18518) hydrogen bonds : bond 0.03869 / 2.57 ( 640) hydrogen bonds : angle 3.94717 / 2.72 ( 1760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.445 Fit side-chains REVERT: A 166 MET cc_start: 0.8599 (tmm) cc_final: 0.8332 (tmm) REVERT: D 48 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8220 (tp30) REVERT: D 65 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8843 (tp-100) REVERT: D 93 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6858 (tm-30) REVERT: D 94 LYS cc_start: 0.8646 (mttp) cc_final: 0.8361 (mptt) REVERT: C 138 MET cc_start: 0.8342 (ttm) cc_final: 0.8121 (ttp) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.0918 time to fit residues: 10.8279 Evaluate side-chains 67 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain F residue 637 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 89 optimal weight: 40.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.060383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043528 restraints weight = 56092.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.045261 restraints weight = 25512.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.046349 restraints weight = 16508.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047015 restraints weight = 12807.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047371 restraints weight = 10995.307| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13247 Z= 0.124 Angle : 0.504 7.039 18518 Z= 0.260 Chirality : 0.036 0.203 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.663 173.665 2864 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.63 % Allowed : 10.58 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.24), residues: 1282 helix: 2.09 (0.20), residues: 708 sheet: 0.09 (0.46), residues: 127 loop : -0.81 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.014 0.001 TYR C 108 PHE 0.009 0.001 PHE A 163 TRP 0.007 0.001 TRP F 97 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13247) covalent geometry : angle 0.50417 / 0.26 (18518) hydrogen bonds : bond 0.03453 / 2.30 ( 640) hydrogen bonds : angle 3.68389 / 2.53 ( 1760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.430 Fit side-chains REVERT: A 166 MET cc_start: 0.8572 (tmm) cc_final: 0.8211 (tmm) REVERT: D 65 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8847 (tp-100) REVERT: D 94 LYS cc_start: 0.8633 (mttp) cc_final: 0.8412 (mttt) REVERT: C 108 TYR cc_start: 0.8440 (m-10) cc_final: 0.8235 (m-80) REVERT: F 248 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8837 (mpp) REVERT: F 273 CYS cc_start: 0.7771 (p) cc_final: 0.7569 (m) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.0837 time to fit residues: 10.2610 Evaluate side-chains 73 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 514 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 59 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN F 466 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.060501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.043607 restraints weight = 56866.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045353 restraints weight = 25729.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046436 restraints weight = 16623.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047092 restraints weight = 12935.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047449 restraints weight = 11156.984| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13247 Z= 0.123 Angle : 0.494 7.607 18518 Z= 0.254 Chirality : 0.036 0.196 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.621 174.160 2864 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.21 % Allowed : 11.44 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1282 helix: 2.30 (0.20), residues: 708 sheet: 0.28 (0.47), residues: 127 loop : -0.63 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.013 0.001 TYR C 108 PHE 0.010 0.001 PHE A 163 TRP 0.006 0.001 TRP A 270 HIS 0.005 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13247) covalent geometry : angle 0.49420 / 0.25 (18518) hydrogen bonds : bond 0.03292 / 2.20 ( 640) hydrogen bonds : angle 3.54201 / 2.43 ( 1760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.440 Fit side-chains REVERT: A 166 MET cc_start: 0.8554 (tmm) cc_final: 0.8165 (tmm) REVERT: D 65 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8871 (tp-100) REVERT: D 93 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6806 (tm-30) REVERT: D 94 LYS cc_start: 0.8629 (mttp) cc_final: 0.8339 (mttp) REVERT: F 248 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8875 (mpp) REVERT: F 273 CYS cc_start: 0.7789 (p) cc_final: 0.7570 (m) outliers start: 23 outliers final: 13 residues processed: 77 average time/residue: 0.0846 time to fit residues: 10.4833 Evaluate side-chains 72 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 514 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 132 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 116 optimal weight: 50.0000 chunk 39 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 30.0000 chunk 112 optimal weight: 0.0010 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.060292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.043439 restraints weight = 56456.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.045151 restraints weight = 25625.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046228 restraints weight = 16665.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.046904 restraints weight = 12947.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047243 restraints weight = 11146.267| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13247 Z= 0.142 Angle : 0.509 9.386 18518 Z= 0.259 Chirality : 0.036 0.213 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.645 175.506 2864 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.31 % Allowed : 12.02 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.24), residues: 1282 helix: 2.39 (0.20), residues: 708 sheet: 0.16 (0.46), residues: 134 loop : -0.52 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.033 0.001 TYR C 108 PHE 0.011 0.001 PHE A 163 TRP 0.006 0.001 TRP B 163 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (13247) covalent geometry : angle 0.50903 / 0.26 (18518) hydrogen bonds : bond 0.03322 / 2.21 ( 640) hydrogen bonds : angle 3.55361 / 2.44 ( 1760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.394 Fit side-chains REVERT: A 166 MET cc_start: 0.8552 (tmm) cc_final: 0.8149 (tmm) REVERT: D 65 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8888 (tp-100) REVERT: D 93 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7096 (tm-30) REVERT: D 94 LYS cc_start: 0.8534 (mttp) cc_final: 0.8226 (mttm) REVERT: F 160 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9385 (mm) REVERT: F 248 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8876 (mpp) REVERT: F 273 CYS cc_start: 0.7820 (p) cc_final: 0.7561 (m) REVERT: F 637 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8300 (ppp) outliers start: 24 outliers final: 18 residues processed: 78 average time/residue: 0.0844 time to fit residues: 10.6096 Evaluate side-chains 79 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 637 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 135 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 92 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.060465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043569 restraints weight = 56393.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.045294 restraints weight = 25656.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.046366 restraints weight = 16661.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047022 restraints weight = 13005.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047331 restraints weight = 11229.623| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13247 Z= 0.132 Angle : 0.503 10.454 18518 Z= 0.257 Chirality : 0.036 0.184 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.646 175.636 2864 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.50 % Allowed : 12.69 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.24), residues: 1282 helix: 2.47 (0.20), residues: 705 sheet: 0.20 (0.46), residues: 134 loop : -0.42 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.010 0.001 TYR C 108 PHE 0.011 0.001 PHE C 106 TRP 0.006 0.001 TRP B 163 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13247) covalent geometry : angle 0.50332 / 0.26 (18518) hydrogen bonds : bond 0.03267 / 2.18 ( 640) hydrogen bonds : angle 3.48949 / 2.41 ( 1760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.425 Fit side-chains REVERT: A 166 MET cc_start: 0.8546 (tmm) cc_final: 0.8138 (tmm) REVERT: F 160 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9352 (mm) REVERT: F 248 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8918 (mpp) REVERT: F 273 CYS cc_start: 0.7844 (p) cc_final: 0.7601 (m) REVERT: F 637 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8294 (ppp) outliers start: 26 outliers final: 18 residues processed: 77 average time/residue: 0.0881 time to fit residues: 11.0037 Evaluate side-chains 76 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 637 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 118 optimal weight: 0.0670 chunk 12 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.060167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.043213 restraints weight = 55888.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.044930 restraints weight = 25713.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046001 restraints weight = 16728.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046607 restraints weight = 13006.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047038 restraints weight = 11298.886| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13247 Z= 0.165 Angle : 0.533 13.067 18518 Z= 0.269 Chirality : 0.037 0.359 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.608 173.121 2864 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.31 % Allowed : 12.88 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1282 helix: 2.51 (0.20), residues: 705 sheet: 0.13 (0.45), residues: 134 loop : -0.41 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.011 0.001 TYR C 108 PHE 0.012 0.001 PHE A 163 TRP 0.007 0.001 TRP A 270 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (13247) covalent geometry : angle 0.53325 / 0.27 (18518) hydrogen bonds : bond 0.03361 / 2.24 ( 640) hydrogen bonds : angle 3.56110 / 2.46 ( 1760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.451 Fit side-chains REVERT: A 166 MET cc_start: 0.8559 (tmm) cc_final: 0.8152 (tmm) REVERT: F 160 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9337 (mm) REVERT: F 273 CYS cc_start: 0.7924 (p) cc_final: 0.7622 (m) REVERT: F 637 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8298 (ppp) outliers start: 24 outliers final: 19 residues processed: 74 average time/residue: 0.0811 time to fit residues: 10.0331 Evaluate side-chains 75 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 637 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 4.9990 chunk 89 optimal weight: 40.0000 chunk 76 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.041398 restraints weight = 56508.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.043000 restraints weight = 27491.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.044013 restraints weight = 18404.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.044587 restraints weight = 14567.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.044854 restraints weight = 12752.524| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13247 Z= 0.350 Angle : 0.667 11.517 18518 Z= 0.338 Chirality : 0.041 0.283 2230 Planarity : 0.005 0.051 1937 Dihedral : 10.772 162.045 2864 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.21 % Allowed : 13.17 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1282 helix: 2.26 (0.20), residues: 707 sheet: 0.01 (0.46), residues: 124 loop : -0.63 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 245 TYR 0.013 0.002 TYR C 108 PHE 0.021 0.002 PHE A 163 TRP 0.014 0.002 TRP A 95 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.35 (13247) covalent geometry : angle 0.66682 / 0.34 (18518) hydrogen bonds : bond 0.04232 / 2.82 ( 640) hydrogen bonds : angle 4.01897 / 2.80 ( 1760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.529 Fit side-chains REVERT: A 166 MET cc_start: 0.8622 (tmm) cc_final: 0.8191 (tmm) REVERT: F 160 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9388 (mm) REVERT: F 273 CYS cc_start: 0.8202 (p) cc_final: 0.7644 (m) outliers start: 23 outliers final: 20 residues processed: 73 average time/residue: 0.0798 time to fit residues: 9.8530 Evaluate side-chains 73 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 637 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.059234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.042184 restraints weight = 56342.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.043888 restraints weight = 25816.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044980 restraints weight = 16781.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045581 restraints weight = 13038.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046009 restraints weight = 11303.273| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13247 Z= 0.212 Angle : 0.586 12.202 18518 Z= 0.297 Chirality : 0.038 0.314 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.662 155.479 2864 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.12 % Allowed : 13.37 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1282 helix: 2.31 (0.20), residues: 708 sheet: 0.01 (0.46), residues: 124 loop : -0.59 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.011 0.001 TYR C 108 PHE 0.013 0.001 PHE A 163 TRP 0.007 0.001 TRP A 95 HIS 0.018 0.001 HIS F 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (13247) covalent geometry : angle 0.58596 / 0.30 (18518) hydrogen bonds : bond 0.03763 / 2.50 ( 640) hydrogen bonds : angle 3.80434 / 2.64 ( 1760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.449 Fit side-chains REVERT: A 166 MET cc_start: 0.8607 (tmm) cc_final: 0.8173 (tmm) REVERT: C 30 CYS cc_start: 0.8832 (t) cc_final: 0.8492 (t) REVERT: F 273 CYS cc_start: 0.8133 (p) cc_final: 0.7617 (m) outliers start: 22 outliers final: 19 residues processed: 77 average time/residue: 0.0766 time to fit residues: 9.9477 Evaluate side-chains 77 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 514 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 0.2980 chunk 90 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.060075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.043141 restraints weight = 56363.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.044877 restraints weight = 25752.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.045974 restraints weight = 16700.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046585 restraints weight = 12999.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.046996 restraints weight = 11268.863| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13247 Z= 0.134 Angle : 0.544 12.294 18518 Z= 0.275 Chirality : 0.037 0.315 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.459 146.532 2864 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.63 % Allowed : 13.94 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1282 helix: 2.41 (0.20), residues: 708 sheet: 0.11 (0.46), residues: 124 loop : -0.51 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.018 0.001 TYR F 474 PHE 0.010 0.001 PHE C 129 TRP 0.009 0.001 TRP F 473 HIS 0.011 0.001 HIS F 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13247) covalent geometry : angle 0.54410 / 0.27 (18518) hydrogen bonds : bond 0.03389 / 2.26 ( 640) hydrogen bonds : angle 3.60833 / 2.49 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.16 seconds wall clock time: 33 minutes 50.07 seconds (2030.07 seconds total)