Starting phenix.real_space_refine on Mon Dec 30 07:10:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qp5_18543/12_2024/8qp5_18543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qp5_18543/12_2024/8qp5_18543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qp5_18543/12_2024/8qp5_18543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qp5_18543/12_2024/8qp5_18543.map" model { file = "/net/cci-nas-00/data/ceres_data/8qp5_18543/12_2024/8qp5_18543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qp5_18543/12_2024/8qp5_18543.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 7836 2.51 5 N 2209 2.21 5 O 2476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12554 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4886 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 24, 'TRANS': 589} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2674 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 11, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1036 Classifications: {'peptide': 171} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 71} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 183 Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1744 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 1521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 299, 1516 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 217} Link IDs: {'PTRANS': 2, 'TRANS': 296} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 844 Unresolved non-hydrogen angles: 1088 Unresolved non-hydrogen dihedrals: 721 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 509 Conformer: "B" Number of residues, atoms: 299, 1516 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 217} Link IDs: {'PTRANS': 2, 'TRANS': 296} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 844 Unresolved non-hydrogen angles: 1088 Unresolved non-hydrogen dihedrals: 721 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 509 bond proxies already assigned to first conformer: 1513 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR P1150 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTYR P1150 " occ=0.50 Time building chain proxies: 8.90, per 1000 atoms: 0.71 Number of scatterers: 12554 At special positions: 0 Unit cell: (135.42, 130.24, 128.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 2476 8.00 N 2209 7.00 C 7836 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: 3.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3164 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 22.7% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.791A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.556A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.547A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.809A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.180A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.605A pdb=" N ASP A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 501 " --> pdb=" O ASP A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 501' Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'B' and resid 136 through 139 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.574A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'C' and resid 191 through 209 removed outlier: 3.680A pdb=" N LEU C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 4.241A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.758A pdb=" N VAL D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.584A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.736A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.990A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'P' and resid 1003 through 1022 removed outlier: 3.562A pdb=" N ALA P1008 " --> pdb=" O THR P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1024 through 1029 removed outlier: 3.759A pdb=" N MET P1029 " --> pdb=" O LEU P1025 " (cutoff:3.500A) Processing helix chain 'P' and resid 1136 through 1139 removed outlier: 3.693A pdb=" N LEU P1139 " --> pdb=" O PHE P1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1136 through 1139' Processing helix chain 'P' and resid 1185 through 1189 Processing helix chain 'P' and resid 1282 through 1287 removed outlier: 3.853A pdb=" N TYR P1286 " --> pdb=" O ALA P1282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181 removed outlier: 7.414A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 274 removed outlier: 7.198A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 349 through 355 removed outlier: 4.057A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 781 through 783 removed outlier: 6.267A pdb=" N ALA A 770 " --> pdb=" O PRO A 790 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 772 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA A 788 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU A 774 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER A 786 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 783 removed outlier: 3.571A pdb=" N GLY A 742 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 467 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.549A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 49 removed outlier: 3.633A pdb=" N THR B 45 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.747A pdb=" N ALA B 66 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.682A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.664A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.794A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 253 through 254 removed outlier: 3.798A pdb=" N ALA B 260 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 268 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA B 262 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 295 through 299 removed outlier: 3.661A pdb=" N LEU B 298 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B 306 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB6, first strand: chain 'C' and resid 134 through 136 removed outlier: 3.741A pdb=" N ASP C 136 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.667A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB9, first strand: chain 'P' and resid 1040 through 1051 removed outlier: 3.646A pdb=" N VAL P1103 " --> pdb=" O HIS P1127 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP P1209 " --> pdb=" O GLU P1168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 1182 through 1183 625 hydrogen bonds defined for protein. 1726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 3.59 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: 3877 1.33 - 1.45: 1956 1.45 - 1.57: 6897 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 12793 Sorted by residual: bond pdb=" N ILE C 131 " pdb=" CA ILE C 131 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 8.19e+00 bond pdb=" N ASN C 110 " pdb=" CA ASN C 110 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.18e-02 7.18e+03 8.10e+00 bond pdb=" N LEU C 106 " pdb=" CA LEU C 106 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" N SER C 105 " pdb=" CA SER C 105 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.47e+00 bond pdb=" N LYS C 127 " pdb=" CA LYS C 127 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.79e+00 ... (remaining 12788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 17159 2.10 - 4.21: 258 4.21 - 6.31: 17 6.31 - 8.42: 3 8.42 - 10.52: 3 Bond angle restraints: 17440 Sorted by residual: angle pdb=" C THR A 479 " pdb=" N VAL A 480 " pdb=" CA VAL A 480 " ideal model delta sigma weight residual 121.65 117.82 3.83 9.40e-01 1.13e+00 1.66e+01 angle pdb=" N LEU C 124 " pdb=" CA LEU C 124 " pdb=" C LEU C 124 " ideal model delta sigma weight residual 113.01 108.67 4.34 1.20e+00 6.94e-01 1.31e+01 angle pdb=" CB MET D 227 " pdb=" CG MET D 227 " pdb=" SD MET D 227 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N ASN C 128 " pdb=" CA ASN C 128 " pdb=" C ASN C 128 " ideal model delta sigma weight residual 114.39 109.39 5.00 1.45e+00 4.76e-01 1.19e+01 angle pdb=" CA SER C 105 " pdb=" C SER C 105 " pdb=" O SER C 105 " ideal model delta sigma weight residual 121.87 118.24 3.63 1.16e+00 7.43e-01 9.77e+00 ... (remaining 17435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6855 17.73 - 35.46: 542 35.46 - 53.19: 82 53.19 - 70.92: 18 70.92 - 88.65: 4 Dihedral angle restraints: 7501 sinusoidal: 2526 harmonic: 4975 Sorted by residual: dihedral pdb=" CA VAL A 480 " pdb=" C VAL A 480 " pdb=" N ASP A 481 " pdb=" CA ASP A 481 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU A 717 " pdb=" C GLU A 717 " pdb=" N PHE A 718 " pdb=" CA PHE A 718 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASN A 259 " pdb=" C ASN A 259 " pdb=" N ILE A 260 " pdb=" CA ILE A 260 " ideal model delta harmonic sigma weight residual 180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1336 0.040 - 0.080: 444 0.080 - 0.119: 151 0.119 - 0.159: 15 0.159 - 0.199: 5 Chirality restraints: 1951 Sorted by residual: chirality pdb=" CG LEU D 167 " pdb=" CB LEU D 167 " pdb=" CD1 LEU D 167 " pdb=" CD2 LEU D 167 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PHE A 586 " pdb=" N PHE A 586 " pdb=" C PHE A 586 " pdb=" CB PHE A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA ILE C 131 " pdb=" N ILE C 131 " pdb=" C ILE C 131 " pdb=" CB ILE C 131 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.98e-01 ... (remaining 1948 not shown) Planarity restraints: 2338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 492 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ASN A 492 " -0.041 2.00e-02 2.50e+03 pdb=" O ASN A 492 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 493 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 586 " -0.017 2.00e-02 2.50e+03 1.39e-02 3.36e+00 pdb=" CG PHE A 586 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 586 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 586 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 586 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 586 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 586 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 136 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 137 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 137 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 137 " 0.021 5.00e-02 4.00e+02 ... (remaining 2335 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 292 2.67 - 3.23: 12474 3.23 - 3.79: 19221 3.79 - 4.34: 24775 4.34 - 4.90: 40392 Nonbonded interactions: 97154 Sorted by model distance: nonbonded pdb=" O GLY E 60 " pdb=" OH TYR E 75 " model vdw 2.113 3.040 nonbonded pdb=" O ILE D 238 " pdb=" OG SER D 242 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR A 608 " pdb=" OE1 GLU A 650 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASN A 297 " pdb=" OG1 THR A 299 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR E 39 " pdb=" OD1 ASN E 41 " model vdw 2.196 3.040 ... (remaining 97149 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=0.50 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.003 0.035 12793 Z= 0.216 Angle : 0.626 10.521 17440 Z= 0.346 Chirality : 0.044 0.199 1951 Planarity : 0.004 0.038 2338 Dihedral : 13.403 88.651 4337 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.17 % Allowed : 0.69 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.49 (0.20), residues: 1729 helix: 1.26 (0.28), residues: 310 sheet: -0.76 (0.21), residues: 570 loop : -2.04 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.004 0.001 HIS A 533 PHE 0.031 0.001 PHE A 586 TYR 0.020 0.001 TYR A 230 ARG 0.005 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 1.597 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. REVERT: A 191 ASP cc_start: 0.9102 (p0) cc_final: 0.8773 (p0) REVERT: B 93 TRP cc_start: 0.4473 (p-90) cc_final: 0.4225 (p-90) REVERT: B 123 TYR cc_start: 0.7907 (m-80) cc_final: 0.7540 (m-80) REVERT: B 347 HIS cc_start: 0.7976 (m-70) cc_final: 0.7694 (m-70) REVERT: D 74 ASP cc_start: 0.9310 (m-30) cc_final: 0.9068 (m-30) REVERT: D 105 ILE cc_start: 0.9123 (mm) cc_final: 0.8822 (mm) REVERT: D 232 GLU cc_start: 0.9130 (mp0) cc_final: 0.8887 (mp0) REVERT: E 28 TYR cc_start: 0.8906 (t80) cc_final: 0.8254 (t80) outliers start: 2 outliers final: 1 residues processed: 195 average time/residue: 0.2332 time to fit residues: 68.1056 Evaluate side-chains 155 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.0030 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 155 optimal weight: 50.0000 overall best weight: 3.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 168 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12793 Z= 0.292 Angle : 0.602 8.994 17440 Z= 0.328 Chirality : 0.044 0.182 1951 Planarity : 0.004 0.043 2338 Dihedral : 4.745 23.386 1878 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.17 % Allowed : 7.45 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.20), residues: 1729 helix: 0.71 (0.26), residues: 325 sheet: -0.88 (0.21), residues: 582 loop : -2.09 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 143 HIS 0.004 0.001 HIS A 533 PHE 0.031 0.002 PHE A 586 TYR 0.018 0.002 TYR A 754 ARG 0.005 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. REVERT: A 193 LEU cc_start: 0.9187 (mt) cc_final: 0.8952 (mt) REVERT: A 321 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7714 (mtm-85) REVERT: B 111 LEU cc_start: 0.9087 (mp) cc_final: 0.8863 (mp) REVERT: B 123 TYR cc_start: 0.7994 (m-80) cc_final: 0.7495 (m-80) REVERT: B 346 LEU cc_start: 0.8452 (mp) cc_final: 0.7867 (tt) REVERT: C 78 LYS cc_start: 0.8517 (mttp) cc_final: 0.8206 (mttm) REVERT: D 74 ASP cc_start: 0.9360 (m-30) cc_final: 0.9050 (m-30) REVERT: D 105 ILE cc_start: 0.9254 (mm) cc_final: 0.8929 (mm) REVERT: D 109 MET cc_start: 0.8879 (mtp) cc_final: 0.8503 (mtp) REVERT: D 219 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8166 (tm-30) REVERT: D 232 GLU cc_start: 0.9070 (mp0) cc_final: 0.8778 (mp0) REVERT: E 50 MET cc_start: 0.8093 (ptp) cc_final: 0.7763 (ptp) REVERT: P 1271 ASN cc_start: 0.8020 (t0) cc_final: 0.7406 (t0) outliers start: 2 outliers final: 2 residues processed: 196 average time/residue: 0.2289 time to fit residues: 66.4608 Evaluate side-chains 162 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 105 optimal weight: 50.0000 chunk 42 optimal weight: 0.3980 chunk 155 optimal weight: 50.0000 chunk 168 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 154 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12793 Z= 0.322 Angle : 0.623 8.188 17440 Z= 0.338 Chirality : 0.044 0.170 1951 Planarity : 0.005 0.093 2338 Dihedral : 4.861 23.456 1878 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.81 (0.20), residues: 1729 helix: 0.61 (0.27), residues: 325 sheet: -0.91 (0.21), residues: 576 loop : -2.18 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 143 HIS 0.003 0.001 HIS A 533 PHE 0.024 0.002 PHE A 586 TYR 0.024 0.002 TYR B 132 ARG 0.007 0.001 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. REVERT: A 193 LEU cc_start: 0.9261 (mt) cc_final: 0.9009 (mt) REVERT: A 369 MET cc_start: 0.9290 (mmt) cc_final: 0.8884 (mmt) REVERT: B 93 TRP cc_start: 0.4410 (p-90) cc_final: 0.4088 (p-90) REVERT: B 111 LEU cc_start: 0.9118 (mp) cc_final: 0.8889 (mp) REVERT: B 123 TYR cc_start: 0.7967 (m-80) cc_final: 0.7417 (m-80) REVERT: B 132 TYR cc_start: 0.8384 (m-80) cc_final: 0.8166 (m-80) REVERT: B 346 LEU cc_start: 0.8473 (mp) cc_final: 0.7831 (tt) REVERT: B 347 HIS cc_start: 0.8138 (m90) cc_final: 0.7899 (m-70) REVERT: D 74 ASP cc_start: 0.9257 (m-30) cc_final: 0.8979 (m-30) REVERT: D 109 MET cc_start: 0.9007 (mtp) cc_final: 0.8669 (mtp) REVERT: E 50 MET cc_start: 0.7726 (ptp) cc_final: 0.7308 (ptp) REVERT: P 1271 ASN cc_start: 0.7960 (t0) cc_final: 0.7245 (t0) outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.2404 time to fit residues: 70.3908 Evaluate side-chains 161 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 50.0000 chunk 116 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 0.0980 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12793 Z= 0.259 Angle : 0.597 9.683 17440 Z= 0.322 Chirality : 0.044 0.182 1951 Planarity : 0.004 0.050 2338 Dihedral : 4.779 22.916 1878 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.20), residues: 1729 helix: 0.84 (0.27), residues: 322 sheet: -0.93 (0.21), residues: 581 loop : -2.16 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.002 0.001 HIS A 533 PHE 0.027 0.002 PHE A 586 TYR 0.020 0.002 TYR D 67 ARG 0.006 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. REVERT: A 193 LEU cc_start: 0.9211 (mt) cc_final: 0.8988 (mt) REVERT: A 646 MET cc_start: 0.8453 (ptp) cc_final: 0.8107 (ptp) REVERT: A 649 TYR cc_start: 0.8655 (p90) cc_final: 0.8450 (p90) REVERT: B 93 TRP cc_start: 0.4558 (p-90) cc_final: 0.4231 (p-90) REVERT: B 111 LEU cc_start: 0.9134 (mp) cc_final: 0.8920 (mp) REVERT: B 123 TYR cc_start: 0.7950 (m-80) cc_final: 0.7325 (m-80) REVERT: B 132 TYR cc_start: 0.8321 (m-80) cc_final: 0.8061 (m-80) REVERT: B 347 HIS cc_start: 0.8155 (m90) cc_final: 0.7765 (m-70) REVERT: C 195 GLN cc_start: 0.7335 (pp30) cc_final: 0.6874 (pp30) REVERT: D 74 ASP cc_start: 0.9238 (m-30) cc_final: 0.8956 (m-30) REVERT: D 109 MET cc_start: 0.9009 (mtp) cc_final: 0.8676 (mtp) REVERT: D 219 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8155 (tm-30) REVERT: D 232 GLU cc_start: 0.9087 (mp0) cc_final: 0.8838 (mp0) REVERT: P 1271 ASN cc_start: 0.7949 (t0) cc_final: 0.7302 (t0) outliers start: 1 outliers final: 1 residues processed: 207 average time/residue: 0.2364 time to fit residues: 72.7204 Evaluate side-chains 160 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12793 Z= 0.226 Angle : 0.584 9.339 17440 Z= 0.313 Chirality : 0.044 0.170 1951 Planarity : 0.004 0.039 2338 Dihedral : 4.675 21.997 1878 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.68 (0.20), residues: 1729 helix: 0.91 (0.27), residues: 322 sheet: -0.92 (0.21), residues: 585 loop : -2.10 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 143 HIS 0.002 0.001 HIS A 186 PHE 0.029 0.002 PHE A 586 TYR 0.016 0.001 TYR A 468 ARG 0.006 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.504 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. REVERT: A 369 MET cc_start: 0.9317 (mmt) cc_final: 0.8967 (mmt) REVERT: A 650 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8853 (mt-10) REVERT: B 111 LEU cc_start: 0.9052 (mp) cc_final: 0.8836 (mp) REVERT: B 123 TYR cc_start: 0.7967 (m-80) cc_final: 0.7321 (m-80) REVERT: B 347 HIS cc_start: 0.8163 (m90) cc_final: 0.7776 (m-70) REVERT: C 195 GLN cc_start: 0.7392 (pp30) cc_final: 0.6891 (pp30) REVERT: D 54 GLN cc_start: 0.8626 (tt0) cc_final: 0.8400 (tt0) REVERT: D 74 ASP cc_start: 0.9225 (m-30) cc_final: 0.8960 (m-30) REVERT: D 109 MET cc_start: 0.8993 (mtp) cc_final: 0.8656 (mtp) REVERT: D 219 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8070 (tm-30) REVERT: P 1271 ASN cc_start: 0.7906 (t0) cc_final: 0.7428 (t0) outliers start: 1 outliers final: 1 residues processed: 207 average time/residue: 0.2467 time to fit residues: 75.4883 Evaluate side-chains 164 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 40.0000 chunk 32 optimal weight: 0.2980 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 165 optimal weight: 0.1980 chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12793 Z= 0.156 Angle : 0.558 9.037 17440 Z= 0.296 Chirality : 0.043 0.174 1951 Planarity : 0.004 0.039 2338 Dihedral : 4.468 20.147 1878 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.20), residues: 1729 helix: 1.23 (0.28), residues: 318 sheet: -0.82 (0.21), residues: 583 loop : -2.00 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 143 HIS 0.004 0.000 HIS D 139 PHE 0.028 0.001 PHE A 586 TYR 0.021 0.001 TYR D 184 ARG 0.004 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. REVERT: A 369 MET cc_start: 0.9322 (mmt) cc_final: 0.8987 (mmt) REVERT: A 428 PHE cc_start: 0.7990 (t80) cc_final: 0.7589 (t80) REVERT: A 646 MET cc_start: 0.8251 (ptp) cc_final: 0.8011 (ptp) REVERT: B 93 TRP cc_start: 0.4438 (p-90) cc_final: 0.4159 (p-90) REVERT: B 123 TYR cc_start: 0.7945 (m-80) cc_final: 0.7346 (m-80) REVERT: B 347 HIS cc_start: 0.8117 (m90) cc_final: 0.7874 (m-70) REVERT: C 195 GLN cc_start: 0.7434 (pp30) cc_final: 0.6959 (pp30) REVERT: D 74 ASP cc_start: 0.9177 (m-30) cc_final: 0.8887 (m-30) REVERT: D 109 MET cc_start: 0.8932 (mtp) cc_final: 0.8478 (mtp) REVERT: D 219 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 236 LYS cc_start: 0.9286 (ptmt) cc_final: 0.8921 (ptmm) REVERT: P 1271 ASN cc_start: 0.7836 (t0) cc_final: 0.7408 (t0) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.2395 time to fit residues: 74.7948 Evaluate side-chains 163 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12793 Z= 0.296 Angle : 0.631 9.293 17440 Z= 0.338 Chirality : 0.044 0.159 1951 Planarity : 0.005 0.043 2338 Dihedral : 4.792 23.651 1878 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.09 % Allowed : 2.17 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.20), residues: 1729 helix: 0.79 (0.27), residues: 322 sheet: -0.92 (0.21), residues: 585 loop : -2.15 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.004 0.001 HIS D 139 PHE 0.029 0.002 PHE A 586 TYR 0.018 0.002 TYR A 468 ARG 0.004 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.655 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. REVERT: A 193 LEU cc_start: 0.9202 (mt) cc_final: 0.8982 (mt) REVERT: A 321 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7571 (mtm-85) REVERT: A 650 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8822 (pt0) REVERT: B 93 TRP cc_start: 0.4515 (p-90) cc_final: 0.4183 (p-90) REVERT: B 123 TYR cc_start: 0.8009 (m-80) cc_final: 0.7346 (m-80) REVERT: B 182 LYS cc_start: 0.9294 (mmtp) cc_final: 0.9000 (mmtp) REVERT: B 347 HIS cc_start: 0.8135 (m90) cc_final: 0.7874 (m-70) REVERT: C 195 GLN cc_start: 0.7441 (pp30) cc_final: 0.6950 (pp30) REVERT: D 56 GLU cc_start: 0.9115 (pt0) cc_final: 0.8907 (pt0) REVERT: D 74 ASP cc_start: 0.9197 (m-30) cc_final: 0.8889 (m-30) REVERT: D 219 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8120 (tm-30) REVERT: D 232 GLU cc_start: 0.9024 (mp0) cc_final: 0.8518 (mp0) REVERT: P 1271 ASN cc_start: 0.7976 (t0) cc_final: 0.7504 (t0) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.2402 time to fit residues: 71.2121 Evaluate side-chains 158 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 30.0000 chunk 98 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12793 Z= 0.186 Angle : 0.588 10.336 17440 Z= 0.312 Chirality : 0.044 0.205 1951 Planarity : 0.004 0.048 2338 Dihedral : 4.581 20.363 1878 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.09 % Allowed : 1.13 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1729 helix: 1.02 (0.27), residues: 322 sheet: -0.86 (0.21), residues: 585 loop : -2.06 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 739 HIS 0.003 0.001 HIS D 139 PHE 0.020 0.001 PHE A 586 TYR 0.020 0.001 TYR D 184 ARG 0.008 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 1.480 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. REVERT: A 369 MET cc_start: 0.9235 (mmt) cc_final: 0.8937 (mmt) REVERT: A 372 MET cc_start: 0.8065 (mmm) cc_final: 0.7856 (mmm) REVERT: B 93 TRP cc_start: 0.4576 (p-90) cc_final: 0.4268 (p-90) REVERT: B 111 LEU cc_start: 0.8890 (mp) cc_final: 0.8638 (mp) REVERT: B 123 TYR cc_start: 0.7980 (m-80) cc_final: 0.7300 (m-80) REVERT: B 182 LYS cc_start: 0.9259 (mmtp) cc_final: 0.9049 (mmtp) REVERT: B 347 HIS cc_start: 0.8095 (m90) cc_final: 0.7858 (m-70) REVERT: C 195 GLN cc_start: 0.7431 (pp30) cc_final: 0.6998 (pp30) REVERT: D 74 ASP cc_start: 0.9163 (m-30) cc_final: 0.8852 (m-30) REVERT: D 105 ILE cc_start: 0.9217 (mm) cc_final: 0.8684 (mm) REVERT: D 109 MET cc_start: 0.8870 (mtp) cc_final: 0.8600 (mtp) REVERT: D 219 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8091 (tm-30) REVERT: D 232 GLU cc_start: 0.9001 (mp0) cc_final: 0.8775 (mp0) REVERT: P 1271 ASN cc_start: 0.7980 (t0) cc_final: 0.7411 (t0) outliers start: 1 outliers final: 1 residues processed: 206 average time/residue: 0.2313 time to fit residues: 71.1136 Evaluate side-chains 164 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 30.0000 chunk 157 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 120 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 138 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12793 Z= 0.341 Angle : 0.665 9.539 17440 Z= 0.356 Chirality : 0.046 0.253 1951 Planarity : 0.005 0.045 2338 Dihedral : 4.923 24.420 1878 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.09 % Allowed : 0.87 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.20), residues: 1729 helix: 0.69 (0.27), residues: 322 sheet: -0.96 (0.21), residues: 586 loop : -2.21 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 776 HIS 0.003 0.001 HIS A 186 PHE 0.022 0.002 PHE A 586 TYR 0.019 0.002 TYR A 468 ARG 0.010 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.561 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9177 (mt) cc_final: 0.8969 (mt) REVERT: A 321 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7641 (mtm110) REVERT: A 369 MET cc_start: 0.9318 (mmt) cc_final: 0.8976 (mmt) REVERT: A 650 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8823 (pt0) REVERT: B 93 TRP cc_start: 0.4756 (p-90) cc_final: 0.4348 (p-90) REVERT: B 123 TYR cc_start: 0.7988 (m-80) cc_final: 0.7252 (m-80) REVERT: B 132 TYR cc_start: 0.8283 (m-80) cc_final: 0.7857 (m-80) REVERT: B 182 LYS cc_start: 0.9273 (mmtp) cc_final: 0.9008 (mmtp) REVERT: B 221 MET cc_start: 0.8034 (ptm) cc_final: 0.7681 (ppp) REVERT: B 347 HIS cc_start: 0.8120 (m90) cc_final: 0.7842 (m-70) REVERT: C 195 GLN cc_start: 0.7442 (pp30) cc_final: 0.6975 (pp30) REVERT: D 56 GLU cc_start: 0.9165 (pt0) cc_final: 0.8902 (pt0) REVERT: D 74 ASP cc_start: 0.9207 (m-30) cc_final: 0.8914 (m-30) REVERT: D 109 MET cc_start: 0.8949 (mtp) cc_final: 0.8706 (mtp) REVERT: D 232 GLU cc_start: 0.9008 (mp0) cc_final: 0.8769 (mp0) REVERT: P 1271 ASN cc_start: 0.8042 (t0) cc_final: 0.7570 (t0) outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.2181 time to fit residues: 64.2890 Evaluate side-chains 163 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 170 optimal weight: 40.0000 chunk 156 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12793 Z= 0.272 Angle : 0.633 9.571 17440 Z= 0.339 Chirality : 0.045 0.225 1951 Planarity : 0.005 0.044 2338 Dihedral : 4.882 22.148 1878 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.81 (0.20), residues: 1729 helix: 0.73 (0.27), residues: 327 sheet: -1.01 (0.21), residues: 573 loop : -2.16 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 776 HIS 0.002 0.001 HIS B 165 PHE 0.030 0.002 PHE A 586 TYR 0.017 0.002 TYR D 67 ARG 0.009 0.001 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 321 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7574 (mtm-85) REVERT: A 369 MET cc_start: 0.9329 (mmt) cc_final: 0.8980 (mmt) REVERT: B 93 TRP cc_start: 0.4701 (p-90) cc_final: 0.4344 (p-90) REVERT: B 123 TYR cc_start: 0.7934 (m-80) cc_final: 0.7154 (m-80) REVERT: B 182 LYS cc_start: 0.9273 (mmtp) cc_final: 0.8998 (mmtp) REVERT: B 221 MET cc_start: 0.7977 (ptm) cc_final: 0.7624 (ppp) REVERT: B 347 HIS cc_start: 0.8119 (m90) cc_final: 0.7835 (m-70) REVERT: C 195 GLN cc_start: 0.7441 (pp30) cc_final: 0.6975 (pp30) REVERT: D 56 GLU cc_start: 0.9149 (pt0) cc_final: 0.8898 (pt0) REVERT: D 74 ASP cc_start: 0.9198 (m-30) cc_final: 0.8872 (m-30) REVERT: D 232 GLU cc_start: 0.8991 (mp0) cc_final: 0.8758 (mp0) REVERT: P 1271 ASN cc_start: 0.8011 (t0) cc_final: 0.7520 (t0) outliers start: 1 outliers final: 1 residues processed: 203 average time/residue: 0.2348 time to fit residues: 71.3239 Evaluate side-chains 165 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN B 368 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.102707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.069109 restraints weight = 45102.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.069849 restraints weight = 29021.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.070192 restraints weight = 19031.341| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12793 Z= 0.165 Angle : 0.607 12.199 17440 Z= 0.317 Chirality : 0.044 0.182 1951 Planarity : 0.004 0.043 2338 Dihedral : 4.591 20.644 1878 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1729 helix: 1.08 (0.28), residues: 326 sheet: -0.86 (0.21), residues: 596 loop : -2.11 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 143 HIS 0.002 0.000 HIS D 139 PHE 0.029 0.001 PHE A 586 TYR 0.020 0.001 TYR B 132 ARG 0.007 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.95 seconds wall clock time: 47 minutes 33.89 seconds (2853.89 seconds total)