Starting phenix.real_space_refine on Sat Sep 12 02:04:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ozs_13134/09_2026/7ozs_13134.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozs_13134/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ozs_13134/09_2026/7ozs_13134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozs_13134/09_2026/7ozs_13134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ozs_13134/09_2026/7ozs_13134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozs_13134/09_2026/7ozs_13134.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ozs_13134/09_2026/7ozs_13134.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ozs_13134/09_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-2.2.1-6174/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: {'RNAv2': 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: 2.55, per 1000 atoms: 0.20 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: 1.05 Conformation dependent library (CDL) restraints added in 468.2 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: 1.52 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: 2.31 Time building geometry restraints manager: 1.41 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: 18107 2.77 - 5.54: 361 5.54 - 8.30: 39 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=" C3' G 3 52 " pdb=" O3' G 3 52 " pdb=" P U 3 53 " ideal model delta sigma weight residual 119.70 125.46 -5.76 1.20e+00 6.94e-01 2.30e+01 ... (remaining 18513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.80: 7417 31.80 - 63.61: 334 63.61 - 95.41: 23 95.41 - 127.21: 0 127.21 - 159.02: 1 Dihedral angle restraints: 7775 sinusoidal: 3884 harmonic: 3891 Sorted by residual: dihedral pdb=" C4' G 3 76 " pdb=" C3' G 3 76 " pdb=" C2' G 3 76 " pdb=" C1' G 3 76 " ideal model delta sinusoidal sigma weight residual 36.35 -37.71 74.05 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' U 3 54 " pdb=" C3' U 3 54 " pdb=" C2' U 3 54 " pdb=" C1' U 3 54 " ideal model delta sinusoidal sigma weight residual 36.34 -36.11 72.45 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' A 3 32 " pdb=" C3' A 3 32 " pdb=" C2' A 3 32 " pdb=" C1' A 3 32 " ideal model delta sinusoidal sigma weight residual 36.34 -35.43 71.77 1 3.10e+00 1.04e-01 6.86e+02 ... (remaining 7772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1840 0.069 - 0.138: 220 0.138 - 0.207: 24 0.207 - 0.276: 139 0.276 - 0.345: 7 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 -2.50 -2.15 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C3' G 3 76 " pdb=" C4' G 3 76 " pdb=" O3' G 3 76 " pdb=" C2' G 3 76 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" P U 3 53 " pdb=" OP1 U 3 53 " pdb=" OP2 U 3 53 " pdb=" O5' U 3 53 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.74e+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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- 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= 0.204 Angle : 0.883 13.842 18518 Z= 0.444 Chirality : 0.075 0.345 2230 Planarity : 0.006 0.073 1937 Dihedral : 15.722 159.017 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 0.00400 / 0.20 (13247) covalent geometry : angle 0.88328 / 0.44 (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 : 0.482 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: 0.0912 time to fit residues: 12.6327 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 : 0.435 ------------------------------------------------------------------------------- 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: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.058870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.042077 restraints weight = 57073.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.043691 restraints weight = 27550.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.044713 restraints weight = 18319.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.045320 restraints weight = 14417.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045654 restraints weight = 12513.049| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 13247 Z= 0.390 Angle : 1.012 18.025 18518 Z= 0.443 Chirality : 0.076 1.228 2230 Planarity : 0.005 0.052 1937 Dihedral : 13.651 166.083 2867 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.15 % Allowed : 7.60 % Favored : 91.25 % 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: 0.38 (0.23), residues: 1282 helix: 1.21 (0.19), residues: 704 sheet: -0.16 (0.45), residues: 136 loop : -1.13 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 173 TYR 0.021 0.002 TYR A 201 PHE 0.021 0.002 PHE C 149 TRP 0.012 0.002 TRP A 95 HIS 0.008 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.39 (13247) covalent geometry : angle 1.01246 / 0.44 (18518) hydrogen bonds : bond 0.04836 / 3.21 ( 640) hydrogen bonds : angle 4.45912 / 3.08 ( 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 : 0.458 Fit side-chains REVERT: A 166 MET cc_start: 0.8650 (tmm) cc_final: 0.8334 (tmm) REVERT: D 48 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8332 (tp30) REVERT: D 93 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6760 (tm-30) REVERT: D 94 LYS cc_start: 0.8695 (mttp) cc_final: 0.8463 (mptt) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.0892 time to fit residues: 9.8845 Evaluate side-chains 63 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL 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: 0.9990 chunk 11 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 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 = 0.3350 r_free = 0.3350 target = 0.060583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.043973 restraints weight = 56641.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045697 restraints weight = 25832.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046822 restraints weight = 16709.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.047502 restraints weight = 12845.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.047855 restraints weight = 10970.895| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13247 Z= 0.152 Angle : 0.769 14.111 18518 Z= 0.335 Chirality : 0.058 0.678 2230 Planarity : 0.004 0.052 1937 Dihedral : 13.730 162.491 2864 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.15 % Allowed : 9.23 % Favored : 89.62 % 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: 1.02 (0.24), residues: 1282 helix: 1.81 (0.20), residues: 706 sheet: -0.02 (0.46), residues: 135 loop : -0.97 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 54 TYR 0.013 0.001 TYR A 201 PHE 0.010 0.001 PHE A 163 TRP 0.020 0.001 TRP F 97 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (13247) covalent geometry : angle 0.76874 / 0.33 (18518) hydrogen bonds : bond 0.03803 / 2.52 ( 640) hydrogen bonds : angle 3.90482 / 2.69 ( 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 77 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.436 Fit side-chains REVERT: A 166 MET cc_start: 0.8602 (tmm) cc_final: 0.8340 (tmm) REVERT: D 65 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8840 (tp-100) REVERT: D 93 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6746 (tm-30) REVERT: D 94 LYS cc_start: 0.8597 (mttp) cc_final: 0.8363 (mptt) REVERT: F 273 CYS cc_start: 0.7754 (p) cc_final: 0.7531 (m) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.0740 time to fit residues: 8.8971 Evaluate side-chains 66 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain D residue 23 PHE 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 246 VAL Chi-restraints excluded: chain C residue 249 HIS 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: 5.9990 chunk 105 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 89 optimal weight: 40.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.059182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.042425 restraints weight = 56391.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044133 restraints weight = 25940.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045188 restraints weight = 16770.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045838 restraints weight = 13059.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.046237 restraints weight = 11239.931| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13247 Z= 0.283 Angle : 0.841 13.659 18518 Z= 0.370 Chirality : 0.060 0.716 2230 Planarity : 0.004 0.049 1937 Dihedral : 13.726 165.672 2864 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.63 % Allowed : 10.96 % Favored : 87.40 % 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: 1.20 (0.24), residues: 1282 helix: 2.00 (0.20), residues: 702 sheet: -0.21 (0.44), residues: 140 loop : -0.84 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 54 TYR 0.016 0.001 TYR A 201 PHE 0.018 0.002 PHE A 163 TRP 0.009 0.002 TRP B 163 HIS 0.006 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.28 (13247) covalent geometry : angle 0.84135 / 0.37 (18518) hydrogen bonds : bond 0.04120 / 2.74 ( 640) hydrogen bonds : angle 4.00870 / 2.78 ( 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 74 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.425 Fit side-chains REVERT: A 166 MET cc_start: 0.8625 (tmm) cc_final: 0.8260 (tmm) REVERT: C 108 TYR cc_start: 0.8486 (m-10) cc_final: 0.8283 (m-10) REVERT: F 248 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8879 (mpp) REVERT: F 273 CYS cc_start: 0.7882 (p) cc_final: 0.7590 (m) outliers start: 17 outliers final: 14 residues processed: 69 average time/residue: 0.0848 time to fit residues: 9.7667 Evaluate side-chains 69 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 637 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 59 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 70 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.061039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.044532 restraints weight = 56774.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046283 restraints weight = 25833.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047396 restraints weight = 16596.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048031 restraints weight = 12774.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048482 restraints weight = 10994.975| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2204 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= 0.128 Angle : 0.714 12.479 18518 Z= 0.313 Chirality : 0.055 0.466 2230 Planarity : 0.004 0.051 1937 Dihedral : 13.884 170.684 2864 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.83 % Allowed : 12.31 % Favored : 85.87 % 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: 1.55 (0.24), residues: 1282 helix: 2.25 (0.20), residues: 707 sheet: 0.25 (0.46), residues: 127 loop : -0.76 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.014 0.001 TYR C 108 PHE 0.009 0.001 PHE C 129 TRP 0.010 0.001 TRP F 473 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13247) covalent geometry : angle 0.71397 / 0.31 (18518) hydrogen bonds : bond 0.03411 / 2.27 ( 640) hydrogen bonds : angle 3.61028 / 2.49 ( 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 80 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.431 Fit side-chains REVERT: A 166 MET cc_start: 0.8576 (tmm) cc_final: 0.8198 (tmm) REVERT: D 65 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8852 (tp-100) REVERT: D 93 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6907 (tm-30) REVERT: D 94 LYS cc_start: 0.8556 (mttp) cc_final: 0.8352 (mttp) REVERT: F 248 MET cc_start: 0.9103 (mtp) cc_final: 0.8828 (mpp) REVERT: F 273 CYS cc_start: 0.7848 (p) cc_final: 0.7597 (m) outliers start: 19 outliers final: 12 residues processed: 77 average time/residue: 0.0838 time to fit residues: 10.7297 Evaluate side-chains 69 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 23 PHE 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 77 VAL Chi-restraints excluded: chain F residue 243 ASP 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: 9.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 14 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 116 optimal weight: 50.0000 chunk 39 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.060829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.044235 restraints weight = 56628.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045982 restraints weight = 25836.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.047044 restraints weight = 16667.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047770 restraints weight = 12959.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.048135 restraints weight = 11057.769| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2322 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= 0.149 Angle : 0.723 12.762 18518 Z= 0.315 Chirality : 0.054 0.396 2230 Planarity : 0.004 0.050 1937 Dihedral : 13.923 173.284 2864 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.12 % Allowed : 12.60 % Favored : 85.29 % 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: 1.72 (0.24), residues: 1282 helix: 2.37 (0.20), residues: 709 sheet: 0.08 (0.46), residues: 134 loop : -0.58 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.028 0.001 TYR C 108 PHE 0.010 0.001 PHE A 163 TRP 0.006 0.001 TRP A 270 HIS 0.004 0.001 HIS F 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (13247) covalent geometry : angle 0.72296 / 0.32 (18518) hydrogen bonds : bond 0.03437 / 2.29 ( 640) hydrogen bonds : angle 3.59006 / 2.47 ( 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 81 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.360 Fit side-chains REVERT: A 166 MET cc_start: 0.8571 (tmm) cc_final: 0.8160 (tmm) REVERT: D 93 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6917 (tm-30) REVERT: D 94 LYS cc_start: 0.8520 (mttp) cc_final: 0.8197 (mttp) REVERT: F 160 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9368 (mm) REVERT: F 248 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8891 (mpp) REVERT: F 273 CYS cc_start: 0.7876 (p) cc_final: 0.7591 (m) REVERT: F 637 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8293 (ppp) outliers start: 22 outliers final: 17 residues processed: 75 average time/residue: 0.0789 time to fit residues: 9.8105 Evaluate side-chains 77 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain A residue 53 VAL 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 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: 0.7980 chunk 122 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.060536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.043869 restraints weight = 56397.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.045576 restraints weight = 26231.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046669 restraints weight = 17145.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047290 restraints weight = 13303.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047737 restraints weight = 11487.083| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13247 Z= 0.185 Angle : 0.736 13.532 18518 Z= 0.323 Chirality : 0.054 0.429 2230 Planarity : 0.004 0.050 1937 Dihedral : 13.978 176.068 2864 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.40 % Allowed : 12.79 % 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: 1.80 (0.24), residues: 1282 helix: 2.42 (0.20), residues: 706 sheet: 0.05 (0.46), residues: 134 loop : -0.48 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.012 0.001 TYR F 116 PHE 0.012 0.001 PHE C 106 TRP 0.006 0.001 TRP A 270 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (13247) covalent geometry : angle 0.73561 / 0.32 (18518) hydrogen bonds : bond 0.03538 / 2.36 ( 640) hydrogen bonds : angle 3.63079 / 2.50 ( 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 82 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.419 Fit side-chains REVERT: A 166 MET cc_start: 0.8600 (tmm) cc_final: 0.8190 (tmm) REVERT: D 93 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6382 (tm-30) REVERT: F 160 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9328 (mm) REVERT: F 248 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8951 (mpp) REVERT: F 273 CYS cc_start: 0.7930 (p) cc_final: 0.7602 (m) REVERT: F 637 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8026 (tmm) outliers start: 25 outliers final: 19 residues processed: 75 average time/residue: 0.0779 time to fit residues: 9.7035 Evaluate side-chains 78 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain A residue 53 VAL 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 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: 6.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.060607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.043958 restraints weight = 55769.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045682 restraints weight = 26043.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046765 restraints weight = 16963.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047427 restraints weight = 13187.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047782 restraints weight = 11349.129| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2487 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= 0.176 Angle : 0.742 13.488 18518 Z= 0.324 Chirality : 0.054 0.429 2230 Planarity : 0.004 0.050 1937 Dihedral : 13.998 177.511 2864 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.40 % Allowed : 13.46 % Favored : 84.13 % 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: 1.84 (0.24), residues: 1282 helix: 2.47 (0.20), residues: 706 sheet: -0.01 (0.46), residues: 134 loop : -0.44 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.012 0.001 TYR F 116 PHE 0.011 0.001 PHE A 163 TRP 0.006 0.001 TRP A 270 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (13247) covalent geometry : angle 0.74232 / 0.32 (18518) hydrogen bonds : bond 0.03507 / 2.34 ( 640) hydrogen bonds : angle 3.61809 / 2.50 ( 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 81 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.8602 (tmm) cc_final: 0.8187 (tmm) REVERT: D 93 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7072 (tm-30) REVERT: C 105 MET cc_start: 0.7733 (mtp) cc_final: 0.7523 (mtm) REVERT: F 112 CYS cc_start: 0.9295 (m) cc_final: 0.8749 (t) REVERT: F 248 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8954 (mpp) REVERT: F 273 CYS cc_start: 0.7973 (p) cc_final: 0.7599 (m) REVERT: F 637 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8026 (tmm) outliers start: 25 outliers final: 19 residues processed: 76 average time/residue: 0.0882 time to fit residues: 10.9940 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 : 0.426 ------------------------------------------------------------------------------- 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 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 D residue 94 LYS 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 248 MET 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: 0.9990 chunk 89 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 110 optimal weight: 0.4980 chunk 121 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.060574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.043973 restraints weight = 55866.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045691 restraints weight = 25915.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046766 restraints weight = 16871.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047396 restraints weight = 13095.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047835 restraints weight = 11315.226| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13247 Z= 0.182 Angle : 0.748 13.413 18518 Z= 0.328 Chirality : 0.054 0.438 2230 Planarity : 0.004 0.050 1937 Dihedral : 14.030 179.217 2864 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.21 % Allowed : 13.85 % Favored : 83.94 % 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: 1.81 (0.24), residues: 1282 helix: 2.43 (0.20), residues: 706 sheet: 0.11 (0.47), residues: 124 loop : -0.46 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.011 0.001 TYR F 116 PHE 0.012 0.001 PHE C 102 TRP 0.006 0.001 TRP A 270 HIS 0.013 0.001 HIS F 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (13247) covalent geometry : angle 0.74826 / 0.33 (18518) hydrogen bonds : bond 0.03555 / 2.37 ( 640) hydrogen bonds : angle 3.64491 / 2.52 ( 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 79 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.8589 (tmm) cc_final: 0.8160 (tmm) REVERT: F 248 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8964 (mpp) REVERT: F 273 CYS cc_start: 0.8109 (p) cc_final: 0.7622 (m) REVERT: F 637 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8033 (tmm) outliers start: 23 outliers final: 20 residues processed: 74 average time/residue: 0.0832 time to fit residues: 10.1790 Evaluate side-chains 76 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 D residue 94 LYS 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 248 MET 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: 9.9990 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.061222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.044725 restraints weight = 56505.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046491 restraints weight = 25712.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.047598 restraints weight = 16500.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048255 restraints weight = 12728.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048601 restraints weight = 10923.815| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2601 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= 0.136 Angle : 0.731 12.856 18518 Z= 0.319 Chirality : 0.053 0.371 2230 Planarity : 0.004 0.050 1937 Dihedral : 14.042 178.727 2864 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.21 % Allowed : 13.75 % Favored : 84.04 % 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: 1.82 (0.24), residues: 1282 helix: 2.42 (0.20), residues: 705 sheet: 0.10 (0.47), residues: 124 loop : -0.41 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.013 0.001 TYR F 232 PHE 0.009 0.001 PHE C 157 TRP 0.013 0.001 TRP F 97 HIS 0.015 0.001 HIS F 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (13247) covalent geometry : angle 0.73084 / 0.32 (18518) hydrogen bonds : bond 0.03378 / 2.26 ( 640) hydrogen bonds : angle 3.54003 / 2.44 ( 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: 23 poor density : 58 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.8595 (tmm) cc_final: 0.8170 (tmm) REVERT: C 177 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7595 (p0) REVERT: F 273 CYS cc_start: 0.8056 (p) cc_final: 0.7629 (m) REVERT: F 474 TYR cc_start: 0.8922 (m-80) cc_final: 0.8715 (m-80) REVERT: F 637 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8289 (ppp) outliers start: 23 outliers final: 18 residues processed: 75 average time/residue: 0.0885 time to fit residues: 10.7910 Evaluate side-chains 76 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 113 LEU 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 177 ASP 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 637 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.061389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.044935 restraints weight = 56544.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046688 restraints weight = 25747.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047785 restraints weight = 16570.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.048456 restraints weight = 12828.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048816 restraints weight = 10977.312| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13247 Z= 0.136 Angle : 0.726 13.352 18518 Z= 0.316 Chirality : 0.052 0.364 2230 Planarity : 0.004 0.051 1937 Dihedral : 13.987 175.312 2864 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.92 % Allowed : 14.33 % Favored : 83.75 % 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: 1.87 (0.24), residues: 1282 helix: 2.46 (0.20), residues: 706 sheet: 0.08 (0.46), residues: 124 loop : -0.40 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 245 TYR 0.012 0.001 TYR F 232 PHE 0.011 0.001 PHE C 102 TRP 0.012 0.001 TRP F 97 HIS 0.007 0.001 HIS F 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (13247) covalent geometry : angle 0.72566 / 0.32 (18518) hydrogen bonds : bond 0.03330 / 2.24 ( 640) hydrogen bonds : angle 3.49444 / 2.41 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.24 seconds wall clock time: 35 minutes 21.71 seconds (2121.71 seconds total)