Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 19:16:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozs_13134/07_2023/7ozs_13134.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozs_13134/07_2023/7ozs_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozs_13134/07_2023/7ozs_13134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozs_13134/07_2023/7ozs_13134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozs_13134/07_2023/7ozs_13134.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozs_13134/07_2023/7ozs_13134.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 600": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/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: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 4} 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: {'GLN:plan1': 2, 'ASP:plan': 1} 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: {'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 79 Time building chain proxies: 6.70, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 5.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.52 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: 4.44 Time building geometry restraints manager: 5.83 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: 96.00 - 104.97: 725 104.97 - 113.94: 8046 113.94 - 122.91: 8412 122.91 - 131.87: 1293 131.87 - 140.84: 42 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 2.440 nonbonded pdb=" OG1 THR A 62 " pdb=" O ALA A 78 " model vdw 2.311 2.440 nonbonded pdb=" O2' G 3 76 " pdb=" O6 G 3 100 " model vdw 2.316 2.440 nonbonded pdb=" OD2 ASP C 48 " pdb=" OH TYR C 123 " model vdw 2.323 2.440 nonbonded pdb=" O GLU F 416 " pdb=" OG1 THR F 420 " model vdw 2.325 2.440 ... (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 ========== 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 4.090 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 36.410 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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= 0.247 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.351 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 85 average time/residue: 0.2151 time to fit residues: 29.1596 Evaluate side-chains 57 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1619 time to fit residues: 1.9378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 128 optimal weight: 0.0270 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13247 Z= 0.179 Angle : 0.537 6.897 18518 Z= 0.278 Chirality : 0.036 0.161 2230 Planarity : 0.004 0.053 1937 Dihedral : 10.352 163.567 2864 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1282 helix: 1.23 (0.19), residues: 696 sheet: 0.01 (0.46), residues: 139 loop : -1.10 (0.27), residues: 447 *********************** 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 74 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.253 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.2038 time to fit residues: 23.5230 Evaluate side-chains 63 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1132 time to fit residues: 2.5507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 50.0000 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 30.0000 chunk 128 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 63 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 13247 Z= 0.360 Angle : 0.603 6.394 18518 Z= 0.309 Chirality : 0.039 0.188 2230 Planarity : 0.004 0.049 1937 Dihedral : 10.659 166.150 2864 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1282 helix: 1.82 (0.20), residues: 699 sheet: -0.01 (0.46), residues: 136 loop : -0.93 (0.28), residues: 447 *********************** 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 67 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 1.213 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.2018 time to fit residues: 21.6713 Evaluate side-chains 60 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1193 time to fit residues: 3.2986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 137 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 63 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1808 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= 0.195 Angle : 0.512 7.332 18518 Z= 0.264 Chirality : 0.036 0.164 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.570 165.824 2864 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1282 helix: 2.11 (0.20), residues: 708 sheet: 0.09 (0.46), residues: 136 loop : -0.82 (0.29), residues: 438 *********************** 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 71 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.235 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.2054 time to fit residues: 23.0013 Evaluate side-chains 63 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1207 time to fit residues: 3.1822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN D 65 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN F 466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 13247 Z= 0.423 Angle : 0.625 8.819 18518 Z= 0.320 Chirality : 0.039 0.187 2230 Planarity : 0.004 0.049 1937 Dihedral : 10.810 167.316 2864 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1282 helix: 2.10 (0.20), residues: 708 sheet: -0.10 (0.45), residues: 136 loop : -0.87 (0.28), residues: 438 *********************** 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 75 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 1.378 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 73 average time/residue: 0.2015 time to fit residues: 24.3467 Evaluate side-chains 61 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1150 time to fit residues: 3.8061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2130 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= 0.183 Angle : 0.516 7.784 18518 Z= 0.265 Chirality : 0.036 0.157 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.691 165.928 2864 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1282 helix: 2.32 (0.20), residues: 707 sheet: -0.07 (0.45), residues: 142 loop : -0.73 (0.29), residues: 433 *********************** 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 72 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.326 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 69 average time/residue: 0.2013 time to fit residues: 23.1417 Evaluate side-chains 60 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1228 time to fit residues: 3.0873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 76 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 83 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 13247 Z= 0.281 Angle : 0.560 10.420 18518 Z= 0.284 Chirality : 0.037 0.249 2230 Planarity : 0.004 0.050 1937 Dihedral : 10.705 165.371 2864 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1282 helix: 2.36 (0.20), residues: 711 sheet: -0.13 (0.45), residues: 142 loop : -0.74 (0.29), residues: 429 *********************** 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 63 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.281 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 0.2040 time to fit residues: 21.1805 Evaluate side-chains 55 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1206 time to fit residues: 2.0645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7127 > 50: distance: 56 - 110: 6.459 distance: 59 - 123: 11.000 distance: 93 - 94: 4.643 distance: 94 - 95: 5.923 distance: 94 - 97: 5.940 distance: 95 - 96: 4.687 distance: 95 - 102: 3.862 distance: 97 - 98: 5.316 distance: 98 - 99: 6.559 distance: 100 - 101: 8.688 distance: 102 - 103: 4.161 distance: 103 - 104: 4.669 distance: 104 - 105: 8.730 distance: 104 - 107: 5.715 distance: 107 - 108: 5.037 distance: 108 - 111: 4.610 distance: 109 - 110: 4.025 distance: 109 - 115: 7.292 distance: 111 - 112: 9.680 distance: 111 - 113: 5.595 distance: 112 - 114: 6.674 distance: 115 - 116: 5.076 distance: 116 - 117: 5.240 distance: 116 - 119: 7.326 distance: 117 - 118: 4.321 distance: 117 - 123: 6.244 distance: 119 - 120: 11.889 distance: 120 - 121: 13.149 distance: 120 - 122: 7.056 distance: 123 - 124: 4.622 distance: 124 - 125: 3.583 distance: 124 - 127: 7.396 distance: 125 - 126: 3.849 distance: 125 - 131: 3.834 distance: 127 - 128: 6.032 distance: 128 - 130: 8.163 distance: 131 - 132: 6.104 distance: 132 - 133: 11.404 distance: 132 - 135: 5.960 distance: 133 - 134: 4.456 distance: 133 - 138: 8.057 distance: 135 - 136: 8.761 distance: 135 - 137: 6.267 distance: 138 - 139: 11.041 distance: 139 - 140: 4.903 distance: 140 - 141: 13.468 distance: 140 - 142: 6.637 distance: 142 - 143: 4.213 distance: 143 - 144: 4.561 distance: 143 - 146: 8.599 distance: 144 - 145: 17.559 distance: 144 - 150: 5.291 distance: 146 - 147: 15.011 distance: 147 - 148: 8.089 distance: 147 - 149: 13.025 distance: 150 - 151: 11.021 distance: 151 - 152: 28.468 distance: 151 - 154: 34.168 distance: 152 - 153: 12.140 distance: 152 - 155: 4.357 distance: 155 - 156: 11.648 distance: 156 - 157: 5.337 distance: 156 - 159: 3.005 distance: 157 - 158: 3.857 distance: 157 - 166: 4.847 distance: 159 - 160: 7.517 distance: 160 - 161: 4.406 distance: 161 - 162: 6.282 distance: 162 - 163: 9.158 distance: 163 - 164: 6.747 distance: 163 - 165: 6.380