Starting phenix.real_space_refine on Fri Mar 14 04:58:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zk6_14756/03_2025/7zk6_14756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zk6_14756/03_2025/7zk6_14756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zk6_14756/03_2025/7zk6_14756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zk6_14756/03_2025/7zk6_14756.map" model { file = "/net/cci-nas-00/data/ceres_data/7zk6_14756/03_2025/7zk6_14756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zk6_14756/03_2025/7zk6_14756.cif" } resolution = 3.1 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= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 5967 2.51 5 N 1574 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9132 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 29, 'TRANS': 1147} Chain breaks: 1 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 178 Unusual residues: {' MG': 2, 'ATP': 2, 'JIZ': 1, 'JJI': 1, 'Y01': 1} Classifications: {'undetermined': 7, 'water': 4} Link IDs: {None: 10} Time building chain proxies: 5.97, per 1000 atoms: 0.64 Number of scatterers: 9310 At special positions: 0 Unit cell: (71.145, 87.048, 148.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 6 15.00 Mg 2 11.99 O 1720 8.00 N 1574 7.00 C 5967 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 69.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 42 through 79 removed outlier: 3.686A pdb=" N ASP A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 93 through 154 removed outlier: 3.634A pdb=" N THR A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 182 removed outlier: 4.010A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 3.817A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.520A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 256 removed outlier: 3.725A pdb=" N ALA A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 265 through 311 removed outlier: 3.631A pdb=" N ASN A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 323 through 357 removed outlier: 3.645A pdb=" N SER A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 358 through 367 removed outlier: 4.079A pdb=" N ILE A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.833A pdb=" N THR A 518 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 542 Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.547A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.808A pdb=" N ARG A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 625 Processing helix chain 'A' and resid 691 through 698 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 708 through 720 Processing helix chain 'A' and resid 720 through 737 removed outlier: 4.304A pdb=" N PHE A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 795 removed outlier: 3.699A pdb=" N LEU A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 763 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 778 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 825 removed outlier: 3.570A pdb=" N ASP A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 850 removed outlier: 4.332A pdb=" N ILE A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 836 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA A 837 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 847 " --> pdb=" O ILE A 843 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 removed outlier: 4.041A pdb=" N THR A 854 " --> pdb=" O GLY A 850 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 855 " --> pdb=" O TRP A 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 855' Processing helix chain 'A' and resid 856 through 873 Proline residue: A 862 - end of helix removed outlier: 3.589A pdb=" N GLY A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 870 " --> pdb=" O ILE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 899 removed outlier: 4.077A pdb=" N GLU A 885 " --> pdb=" O LYS A 881 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 886 " --> pdb=" O ASP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 907 Processing helix chain 'A' and resid 908 through 962 removed outlier: 4.414A pdb=" N ILE A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) Proline residue: A 923 - end of helix removed outlier: 4.025A pdb=" N HIS A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 945 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 990 removed outlier: 3.986A pdb=" N PHE A 979 " --> pdb=" O SER A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1010 removed outlier: 3.536A pdb=" N HIS A1003 " --> pdb=" O VAL A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.516A pdb=" N VAL A1075 " --> pdb=" O GLY A1071 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1108 removed outlier: 3.822A pdb=" N GLN A1108 " --> pdb=" O TRP A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1128 Processing helix chain 'A' and resid 1129 through 1131 No H-bonds generated for 'chain 'A' and resid 1129 through 1131' Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1157 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.009A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 removed outlier: 3.544A pdb=" N ALA A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1236 removed outlier: 3.717A pdb=" N ASN A1235 " --> pdb=" O THR A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1259 Processing helix chain 'A' and resid 1261 through 1271 removed outlier: 3.641A pdb=" N VAL A1269 " --> pdb=" O SER A1265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A1271 " --> pdb=" O VAL A1267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413 removed outlier: 6.948A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 393 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP A 444 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 3.891A pdb=" N GLU A 604 " --> pdb=" O GLY A 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1049 through 1056 removed outlier: 7.091A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE A1033 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE A1091 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY A1035 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER A1089 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.079A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A1251 " --> pdb=" O ILE A1239 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A1249 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN A1243 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL A1247 " --> pdb=" O GLN A1243 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1749 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: 3.84 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 1508 1.31 - 1.45: 2497 1.45 - 1.59: 5398 1.59 - 1.73: 16 1.73 - 1.87: 67 Bond restraints: 9486 Sorted by residual: bond pdb=" C03 JIZ A2007 " pdb=" N02 JIZ A2007 " ideal model delta sigma weight residual 1.367 1.636 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C13 JIZ A2007 " pdb=" N06 JIZ A2007 " ideal model delta sigma weight residual 1.366 1.616 -0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C08 JIZ A2007 " pdb=" N04 JIZ A2007 " ideal model delta sigma weight residual 1.366 1.614 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" N2 JJI A2006 " pdb=" O22 JJI A2006 " ideal model delta sigma weight residual 1.204 1.405 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" N4 JJI A2006 " pdb=" O42 JJI A2006 " ideal model delta sigma weight residual 1.207 1.407 -0.200 2.00e-02 2.50e+03 9.95e+01 ... (remaining 9481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 12764 4.03 - 8.05: 68 8.05 - 12.08: 11 12.08 - 16.11: 3 16.11 - 20.14: 4 Bond angle restraints: 12850 Sorted by residual: angle pdb=" N SER A 92 " pdb=" CA SER A 92 " pdb=" C SER A 92 " ideal model delta sigma weight residual 113.01 103.19 9.82 1.20e+00 6.94e-01 6.69e+01 angle pdb=" N VAL A 84 " pdb=" CA VAL A 84 " pdb=" C VAL A 84 " ideal model delta sigma weight residual 113.00 102.89 10.11 1.30e+00 5.92e-01 6.05e+01 angle pdb=" C18 JJI A2006 " pdb=" S04 JJI A2006 " pdb=" S JJI A2006 " ideal model delta sigma weight residual 102.75 122.89 -20.14 3.00e+00 1.11e-01 4.50e+01 angle pdb=" C12 JIZ A2007 " pdb=" S03 JIZ A2007 " pdb=" C14 JIZ A2007 " ideal model delta sigma weight residual 89.68 107.29 -17.61 3.00e+00 1.11e-01 3.45e+01 angle pdb=" C07 JIZ A2007 " pdb=" S02 JIZ A2007 " pdb=" C09 JIZ A2007 " ideal model delta sigma weight residual 89.67 107.20 -17.53 3.00e+00 1.11e-01 3.42e+01 ... (remaining 12845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5189 17.99 - 35.97: 412 35.97 - 53.96: 86 53.96 - 71.95: 34 71.95 - 89.93: 7 Dihedral angle restraints: 5728 sinusoidal: 2357 harmonic: 3371 Sorted by residual: dihedral pdb=" CA TRP A 311 " pdb=" C TRP A 311 " pdb=" N TYR A 312 " pdb=" CA TYR A 312 " ideal model delta harmonic sigma weight residual -180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PHE A 310 " pdb=" C PHE A 310 " pdb=" N TRP A 311 " pdb=" CA TRP A 311 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" C GLN A 87 " pdb=" N GLN A 87 " pdb=" CA GLN A 87 " pdb=" CB GLN A 87 " ideal model delta harmonic sigma weight residual -122.60 -133.51 10.91 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 5725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 1447 0.150 - 0.299: 18 0.299 - 0.449: 1 0.449 - 0.598: 1 0.598 - 0.748: 1 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C06 JJI A2006 " pdb=" C07 JJI A2006 " pdb=" C16 JJI A2006 " pdb=" N03 JJI A2006 " both_signs ideal model delta sigma weight residual False 2.50 1.75 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" C11 JJI A2006 " pdb=" C12 JJI A2006 " pdb=" C17 JJI A2006 " pdb=" N05 JJI A2006 " both_signs ideal model delta sigma weight residual False 2.38 2.86 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" C06 JIZ A2007 " pdb=" C07 JIZ A2007 " pdb=" C16 JIZ A2007 " pdb=" N03 JIZ A2007 " both_signs ideal model delta sigma weight residual False 2.46 2.76 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1465 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 861 " -0.076 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO A 862 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 862 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 862 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 279 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C GLU A 279 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU A 279 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A 280 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 JJI A2006 " -0.001 2.00e-02 2.50e+03 1.68e-02 4.94e+00 pdb=" C07 JJI A2006 " -0.017 2.00e-02 2.50e+03 pdb=" C08 JJI A2006 " 0.027 2.00e-02 2.50e+03 pdb=" C09 JJI A2006 " 0.005 2.00e-02 2.50e+03 pdb=" C10 JJI A2006 " -0.025 2.00e-02 2.50e+03 pdb=" N04 JJI A2006 " 0.016 2.00e-02 2.50e+03 pdb=" S02 JJI A2006 " -0.007 2.00e-02 2.50e+03 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 91 2.61 - 3.19: 8439 3.19 - 3.76: 14643 3.76 - 4.33: 21051 4.33 - 4.90: 33877 Nonbonded interactions: 78101 Sorted by model distance: nonbonded pdb=" O2B ATP A2003 " pdb="MG MG A2004 " model vdw 2.043 2.170 nonbonded pdb="MG MG A2004 " pdb=" O HOH A2101 " model vdw 2.054 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2102 " model vdw 2.054 2.170 nonbonded pdb=" OG SER A 430 " pdb="MG MG A2002 " model vdw 2.067 2.170 nonbonded pdb=" OE1 GLN A 471 " pdb="MG MG A2002 " model vdw 2.070 2.170 ... (remaining 78096 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.009 0.269 9486 Z= 0.575 Angle : 0.899 20.135 12850 Z= 0.500 Chirality : 0.052 0.748 1468 Planarity : 0.005 0.112 1618 Dihedral : 14.768 89.933 3568 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.28 % Cbeta Deviations : 0.09 % 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: 0.33 (0.24), residues: 1173 helix: 0.49 (0.19), residues: 745 sheet: 0.30 (0.58), residues: 75 loop : -0.09 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 851 HIS 0.003 0.000 HIS A 141 PHE 0.022 0.001 PHE A 728 TYR 0.012 0.001 TYR A 949 ARG 0.002 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7009 (mmmt) cc_final: 0.6769 (mmtt) REVERT: A 293 ILE cc_start: 0.7528 (tt) cc_final: 0.7287 (tt) REVERT: A 392 ASN cc_start: 0.8118 (m110) cc_final: 0.7744 (t0) REVERT: A 452 GLN cc_start: 0.7438 (tt0) cc_final: 0.7209 (tt0) REVERT: A 872 MET cc_start: 0.7897 (mmm) cc_final: 0.7438 (ttm) REVERT: A 929 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7229 (tppt) REVERT: A 966 THR cc_start: 0.8519 (p) cc_final: 0.8245 (t) REVERT: A 1246 LYS cc_start: 0.7811 (mptt) cc_final: 0.7283 (mtmm) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.2708 time to fit residues: 86.1652 Evaluate side-chains 164 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 0.0020 overall best weight: 0.4906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 292 ASN A 700 ASN A1032 GLN A1171 GLN A1234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.190661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156523 restraints weight = 10775.050| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.19 r_work: 0.3661 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9486 Z= 0.205 Angle : 0.571 6.537 12850 Z= 0.306 Chirality : 0.042 0.285 1468 Planarity : 0.005 0.060 1618 Dihedral : 9.988 79.571 1450 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.04 % Allowed : 8.70 % Favored : 90.27 % 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: 0.71 (0.24), residues: 1173 helix: 0.80 (0.19), residues: 773 sheet: 0.39 (0.57), residues: 75 loop : -0.04 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 851 HIS 0.008 0.001 HIS A 141 PHE 0.016 0.001 PHE A 990 TYR 0.019 0.001 TYR A 949 ARG 0.007 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.7456 (tpp) cc_final: 0.7254 (tpp) REVERT: A 209 LYS cc_start: 0.7046 (mmmt) cc_final: 0.6703 (mmtt) REVERT: A 293 ILE cc_start: 0.7425 (tt) cc_final: 0.7219 (tt) REVERT: A 391 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7570 (pttp) REVERT: A 452 GLN cc_start: 0.7593 (tt0) cc_final: 0.7287 (tt0) REVERT: A 851 TRP cc_start: 0.8579 (p-90) cc_final: 0.8368 (p-90) REVERT: A 872 MET cc_start: 0.8439 (mmm) cc_final: 0.7792 (ttm) REVERT: A 882 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6424 (m-30) REVERT: A 966 THR cc_start: 0.8504 (p) cc_final: 0.8165 (t) REVERT: A 1006 ARG cc_start: 0.7422 (ttm-80) cc_final: 0.6981 (mtm-85) REVERT: A 1108 GLN cc_start: 0.7590 (mp10) cc_final: 0.7385 (mp10) REVERT: A 1164 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6985 (tmt170) outliers start: 10 outliers final: 7 residues processed: 183 average time/residue: 0.2531 time to fit residues: 63.9081 Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 44 optimal weight: 0.0570 chunk 113 optimal weight: 0.0270 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A1234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.192661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156123 restraints weight = 11135.338| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.35 r_work: 0.3655 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9486 Z= 0.170 Angle : 0.522 8.597 12850 Z= 0.278 Chirality : 0.040 0.176 1468 Planarity : 0.004 0.059 1618 Dihedral : 9.263 77.036 1450 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.45 % Allowed : 11.90 % Favored : 86.65 % 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: 0.90 (0.24), residues: 1173 helix: 0.97 (0.19), residues: 774 sheet: 0.50 (0.57), residues: 75 loop : -0.03 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 851 HIS 0.006 0.001 HIS A 141 PHE 0.014 0.001 PHE A 508 TYR 0.016 0.001 TYR A 949 ARG 0.006 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: A 209 LYS cc_start: 0.6920 (mmmt) cc_final: 0.6654 (mmtt) REVERT: A 293 ILE cc_start: 0.7311 (tt) cc_final: 0.7106 (tt) REVERT: A 391 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7510 (pttp) REVERT: A 450 ASP cc_start: 0.7786 (m-30) cc_final: 0.7414 (m-30) REVERT: A 452 GLN cc_start: 0.7616 (tt0) cc_final: 0.7345 (tt0) REVERT: A 836 ILE cc_start: 0.8310 (tt) cc_final: 0.8090 (mt) REVERT: A 872 MET cc_start: 0.8466 (mmm) cc_final: 0.8058 (ttm) REVERT: A 966 THR cc_start: 0.8497 (p) cc_final: 0.8207 (t) REVERT: A 1028 GLU cc_start: 0.7698 (tp30) cc_final: 0.7390 (tp30) REVERT: A 1030 ASN cc_start: 0.7393 (m110) cc_final: 0.7028 (m-40) outliers start: 14 outliers final: 7 residues processed: 168 average time/residue: 0.2360 time to fit residues: 54.6617 Evaluate side-chains 159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 892 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 0.0020 chunk 57 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN A1234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.189387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150948 restraints weight = 11143.428| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.25 r_work: 0.3635 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9486 Z= 0.213 Angle : 0.513 6.157 12850 Z= 0.274 Chirality : 0.041 0.217 1468 Planarity : 0.004 0.057 1618 Dihedral : 8.904 83.322 1450 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.28 % Allowed : 12.63 % Favored : 85.09 % 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: 1.07 (0.24), residues: 1173 helix: 1.08 (0.19), residues: 776 sheet: 0.71 (0.61), residues: 70 loop : 0.04 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 851 HIS 0.006 0.001 HIS A 141 PHE 0.018 0.001 PHE A 508 TYR 0.015 0.001 TYR A 949 ARG 0.006 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.6912 (mmmt) cc_final: 0.6641 (mmtt) REVERT: A 268 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7507 (mttp) REVERT: A 293 ILE cc_start: 0.7379 (tt) cc_final: 0.7163 (tt) REVERT: A 391 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7449 (pttp) REVERT: A 450 ASP cc_start: 0.7837 (m-30) cc_final: 0.7515 (m-30) REVERT: A 452 GLN cc_start: 0.7687 (tt0) cc_final: 0.7238 (tt0) REVERT: A 872 MET cc_start: 0.8386 (mmm) cc_final: 0.8095 (ttm) REVERT: A 966 THR cc_start: 0.8514 (p) cc_final: 0.8275 (t) REVERT: A 1028 GLU cc_start: 0.7607 (tp30) cc_final: 0.7376 (tp30) REVERT: A 1091 PHE cc_start: 0.7572 (m-10) cc_final: 0.6908 (m-10) outliers start: 22 outliers final: 17 residues processed: 176 average time/residue: 0.2347 time to fit residues: 57.4828 Evaluate side-chains 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 0.0270 chunk 111 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.188894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152708 restraints weight = 10936.229| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.11 r_work: 0.3654 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9486 Z= 0.173 Angle : 0.495 8.441 12850 Z= 0.265 Chirality : 0.040 0.195 1468 Planarity : 0.004 0.056 1618 Dihedral : 8.635 81.672 1450 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.48 % Allowed : 12.63 % Favored : 84.89 % 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: 1.22 (0.24), residues: 1173 helix: 1.24 (0.19), residues: 776 sheet: 0.67 (0.61), residues: 70 loop : -0.01 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 851 HIS 0.003 0.001 HIS A 141 PHE 0.016 0.001 PHE A 990 TYR 0.014 0.001 TYR A 949 ARG 0.005 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.7513 (tpp) cc_final: 0.7312 (tpp) REVERT: A 209 LYS cc_start: 0.6855 (mmmt) cc_final: 0.6608 (mmtt) REVERT: A 293 ILE cc_start: 0.7355 (tt) cc_final: 0.7137 (tt) REVERT: A 391 LYS cc_start: 0.8163 (ttpp) cc_final: 0.7378 (pttp) REVERT: A 450 ASP cc_start: 0.7977 (m-30) cc_final: 0.7663 (m-30) REVERT: A 452 GLN cc_start: 0.7771 (tt0) cc_final: 0.7278 (tt0) REVERT: A 872 MET cc_start: 0.8498 (mmm) cc_final: 0.8187 (ttm) REVERT: A 966 THR cc_start: 0.8457 (p) cc_final: 0.8216 (t) REVERT: A 1028 GLU cc_start: 0.7848 (tp30) cc_final: 0.7625 (tp30) REVERT: A 1030 ASN cc_start: 0.7668 (m-40) cc_final: 0.7312 (p0) REVERT: A 1091 PHE cc_start: 0.7465 (m-10) cc_final: 0.6853 (m-10) outliers start: 24 outliers final: 16 residues processed: 171 average time/residue: 0.2537 time to fit residues: 60.3814 Evaluate side-chains 166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A1234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.189030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152843 restraints weight = 11069.319| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.24 r_work: 0.3623 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9486 Z= 0.228 Angle : 0.518 7.500 12850 Z= 0.275 Chirality : 0.041 0.192 1468 Planarity : 0.004 0.055 1618 Dihedral : 8.633 87.243 1450 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.90 % Allowed : 13.66 % Favored : 83.44 % 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: 1.17 (0.24), residues: 1173 helix: 1.20 (0.19), residues: 776 sheet: 0.69 (0.62), residues: 70 loop : -0.04 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 851 HIS 0.005 0.001 HIS A 141 PHE 0.019 0.001 PHE A 508 TYR 0.014 0.001 TYR A 949 ARG 0.004 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.6876 (mmmt) cc_final: 0.6623 (mmtt) REVERT: A 293 ILE cc_start: 0.7434 (tt) cc_final: 0.7219 (tt) REVERT: A 450 ASP cc_start: 0.7874 (m-30) cc_final: 0.7576 (m-30) REVERT: A 845 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8206 (tt) REVERT: A 872 MET cc_start: 0.8387 (mmm) cc_final: 0.8182 (ttm) REVERT: A 1028 GLU cc_start: 0.7644 (tp30) cc_final: 0.7412 (tp30) REVERT: A 1030 ASN cc_start: 0.7603 (m-40) cc_final: 0.7384 (p0) REVERT: A 1091 PHE cc_start: 0.7521 (m-10) cc_final: 0.6938 (m-10) outliers start: 28 outliers final: 20 residues processed: 162 average time/residue: 0.2333 time to fit residues: 52.5632 Evaluate side-chains 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.184342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150628 restraints weight = 11146.783| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.05 r_work: 0.3598 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9486 Z= 0.276 Angle : 0.549 7.662 12850 Z= 0.289 Chirality : 0.042 0.191 1468 Planarity : 0.004 0.055 1618 Dihedral : 8.694 87.066 1450 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.31 % Allowed : 13.87 % Favored : 82.82 % 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: 1.06 (0.24), residues: 1173 helix: 1.12 (0.19), residues: 777 sheet: 0.73 (0.62), residues: 70 loop : -0.11 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 311 HIS 0.006 0.001 HIS A 141 PHE 0.020 0.002 PHE A 508 TYR 0.015 0.001 TYR A 949 ARG 0.009 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.971 Fit side-chains REVERT: A 209 LYS cc_start: 0.6875 (mmmt) cc_final: 0.6595 (mmtt) REVERT: A 391 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7486 (pttp) REVERT: A 450 ASP cc_start: 0.7892 (m-30) cc_final: 0.7601 (m-30) REVERT: A 604 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7943 (mt-10) REVERT: A 990 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.2655 (p90) REVERT: A 1028 GLU cc_start: 0.7488 (tp30) cc_final: 0.7251 (tp30) REVERT: A 1091 PHE cc_start: 0.7586 (m-10) cc_final: 0.7075 (m-10) REVERT: A 1096 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7647 (tm-30) outliers start: 32 outliers final: 21 residues processed: 165 average time/residue: 0.2274 time to fit residues: 52.5276 Evaluate side-chains 164 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 106 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.188636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.153374 restraints weight = 11299.487| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.18 r_work: 0.3624 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9486 Z= 0.178 Angle : 0.525 9.883 12850 Z= 0.273 Chirality : 0.040 0.188 1468 Planarity : 0.004 0.055 1618 Dihedral : 8.463 86.818 1450 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.59 % Allowed : 15.01 % Favored : 82.40 % 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: 1.19 (0.24), residues: 1173 helix: 1.29 (0.19), residues: 776 sheet: 0.47 (0.61), residues: 73 loop : -0.21 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 851 HIS 0.004 0.001 HIS A 141 PHE 0.016 0.001 PHE A 990 TYR 0.014 0.001 TYR A 949 ARG 0.010 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.973 Fit side-chains REVERT: A 171 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7792 (tt) REVERT: A 200 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7088 (t80) REVERT: A 209 LYS cc_start: 0.6765 (mmmt) cc_final: 0.6524 (mmtt) REVERT: A 293 ILE cc_start: 0.7385 (tt) cc_final: 0.7183 (tt) REVERT: A 328 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 391 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7446 (pttp) REVERT: A 450 ASP cc_start: 0.7894 (m-30) cc_final: 0.7633 (m-30) REVERT: A 604 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7948 (mt-10) REVERT: A 763 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.5908 (t80) REVERT: A 944 MET cc_start: 0.8495 (tpp) cc_final: 0.8268 (tpp) REVERT: A 990 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.2445 (p90) REVERT: A 1028 GLU cc_start: 0.7669 (tp30) cc_final: 0.7302 (tp30) REVERT: A 1091 PHE cc_start: 0.7489 (m-10) cc_final: 0.6914 (m-10) REVERT: A 1096 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7656 (tm-30) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 0.2416 time to fit residues: 53.2540 Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 20 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.179180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141178 restraints weight = 10961.932| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.24 r_work: 0.3429 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9486 Z= 0.181 Angle : 0.514 9.379 12850 Z= 0.267 Chirality : 0.040 0.202 1468 Planarity : 0.004 0.054 1618 Dihedral : 8.317 85.637 1450 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.90 % Allowed : 14.91 % Favored : 82.19 % 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: 1.29 (0.24), residues: 1173 helix: 1.37 (0.19), residues: 776 sheet: 0.58 (0.62), residues: 70 loop : -0.16 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 851 HIS 0.004 0.001 HIS A 141 PHE 0.015 0.001 PHE A 990 TYR 0.013 0.001 TYR A 949 ARG 0.008 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.026 Fit side-chains REVERT: A 91 MET cc_start: 0.5007 (tmm) cc_final: 0.4728 (tmm) REVERT: A 171 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7389 (tt) REVERT: A 200 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 293 ILE cc_start: 0.7106 (tt) cc_final: 0.6896 (tt) REVERT: A 391 LYS cc_start: 0.7806 (ttpp) cc_final: 0.7140 (pttp) REVERT: A 450 ASP cc_start: 0.7996 (m-30) cc_final: 0.7701 (m-30) REVERT: A 604 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 845 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8045 (tt) REVERT: A 944 MET cc_start: 0.8477 (tpp) cc_final: 0.8215 (tpp) REVERT: A 990 PHE cc_start: 0.4527 (OUTLIER) cc_final: 0.2078 (p90) REVERT: A 1028 GLU cc_start: 0.8000 (tp30) cc_final: 0.7293 (tp30) REVERT: A 1091 PHE cc_start: 0.7260 (m-10) cc_final: 0.6593 (m-10) REVERT: A 1096 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7852 (tm-30) outliers start: 28 outliers final: 21 residues processed: 160 average time/residue: 0.2311 time to fit residues: 51.5175 Evaluate side-chains 166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 75 optimal weight: 0.0570 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144908 restraints weight = 11125.806| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.22 r_work: 0.3462 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9486 Z= 0.149 Angle : 0.495 8.899 12850 Z= 0.259 Chirality : 0.039 0.214 1468 Planarity : 0.004 0.054 1618 Dihedral : 8.071 80.180 1450 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.28 % Allowed : 16.25 % Favored : 81.47 % 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: 1.41 (0.24), residues: 1173 helix: 1.46 (0.19), residues: 775 sheet: 0.67 (0.62), residues: 70 loop : -0.13 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 851 HIS 0.003 0.000 HIS A 141 PHE 0.019 0.001 PHE A 990 TYR 0.012 0.001 TYR A 949 ARG 0.010 0.000 ARG A 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.150 Fit side-chains REVERT: A 391 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7126 (pttp) REVERT: A 450 ASP cc_start: 0.7975 (m-30) cc_final: 0.7689 (m-30) REVERT: A 604 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 763 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.5967 (t80) REVERT: A 845 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8064 (tt) REVERT: A 990 PHE cc_start: 0.4552 (OUTLIER) cc_final: 0.2071 (p90) REVERT: A 1028 GLU cc_start: 0.7992 (tp30) cc_final: 0.7240 (tp30) REVERT: A 1091 PHE cc_start: 0.7189 (m-10) cc_final: 0.6551 (m-10) REVERT: A 1096 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 1108 GLN cc_start: 0.7719 (mp10) cc_final: 0.7445 (mp10) outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 0.2424 time to fit residues: 53.6565 Evaluate side-chains 155 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.0270 chunk 93 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 107 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 105 optimal weight: 0.7980 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.185339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148029 restraints weight = 11025.276| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.22 r_work: 0.3496 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9486 Z= 0.135 Angle : 0.496 9.190 12850 Z= 0.258 Chirality : 0.039 0.242 1468 Planarity : 0.004 0.054 1618 Dihedral : 7.922 77.832 1450 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.28 % Allowed : 16.56 % Favored : 81.16 % 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: 1.53 (0.24), residues: 1173 helix: 1.55 (0.19), residues: 779 sheet: 0.66 (0.63), residues: 70 loop : -0.08 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 851 HIS 0.002 0.000 HIS A 141 PHE 0.025 0.001 PHE A 940 TYR 0.009 0.001 TYR A 949 ARG 0.008 0.000 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4942.74 seconds wall clock time: 87 minutes 46.83 seconds (5266.83 seconds total)