Starting phenix.real_space_refine on Fri Jul 3 03:46:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w41_37260/07_2026/8w41_37260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w41_37260/07_2026/8w41_37260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w41_37260/07_2026/8w41_37260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w41_37260/07_2026/8w41_37260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w41_37260/07_2026/8w41_37260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w41_37260/07_2026/8w41_37260.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 28 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 68 5.16 5 C 7417 2.51 5 N 2071 2.21 5 O 2295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11859 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1156 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "I" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 9515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 9515 Classifications: {'peptide': 1162} Link IDs: {'PTRANS': 37, 'TRANS': 1124} Chain breaks: 4 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.17, per 1000 atoms: 0.18 Number of scatterers: 11859 At special positions: 0 Unit cell: (74.43, 102.548, 186.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 68 16.00 P 3 15.00 Mg 1 11.99 O 2295 8.00 N 2071 7.00 C 7417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 377.9 milliseconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 63.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 6 through 21 Processing helix chain 'B' and resid 29 through 40 removed outlier: 4.096A pdb=" N LEU B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.562A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.661A pdb=" N ASP B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'I' and resid 6 through 20 Processing helix chain 'I' and resid 29 through 38 removed outlier: 4.180A pdb=" N THR I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 57 Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 65 through 79 removed outlier: 4.046A pdb=" N ASP I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 93 removed outlier: 4.003A pdb=" N PHE I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 113 Processing helix chain 'I' and resid 118 through 129 removed outlier: 3.710A pdb=" N VAL I 122 " --> pdb=" O THR I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 148 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.520A pdb=" N SER A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.517A pdb=" N TYR A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.504A pdb=" N ILE A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.566A pdb=" N ASN A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.761A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.883A pdb=" N CYS A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.077A pdb=" N ARG A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.665A pdb=" N GLY A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 350 " --> pdb=" O HIS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.445A pdb=" N GLN A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 removed outlier: 3.583A pdb=" N THR A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 443 removed outlier: 3.769A pdb=" N PHE A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 489 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 511 through 520 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 539 through 551 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.549A pdb=" N GLU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 642 through 661 Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.518A pdb=" N ILE A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 711 through 720 removed outlier: 3.879A pdb=" N LYS A 720 " --> pdb=" O ASN A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.666A pdb=" N ARG A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 removed outlier: 3.561A pdb=" N PHE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 3.750A pdb=" N GLN A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 829 removed outlier: 3.994A pdb=" N VAL A 796 " --> pdb=" O ARG A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 860 removed outlier: 3.982A pdb=" N GLU A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 888 removed outlier: 3.709A pdb=" N MET A 867 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 920 removed outlier: 3.558A pdb=" N LYS A 904 " --> pdb=" O ASP A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 979 removed outlier: 3.935A pdb=" N ARG A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 963 " --> pdb=" O GLU A 959 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1021 removed outlier: 3.605A pdb=" N ARG A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 3.511A pdb=" N LEU A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1119 removed outlier: 3.630A pdb=" N ALA A1100 " --> pdb=" O GLU A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1136 Processing helix chain 'A' and resid 1177 through 1181 removed outlier: 3.888A pdb=" N GLN A1181 " --> pdb=" O PRO A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 Processing helix chain 'A' and resid 1245 through 1255 removed outlier: 3.644A pdb=" N PHE A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1268 Processing sheet with id=AA1, first strand: chain 'I' and resid 100 through 101 removed outlier: 3.530A pdb=" N VAL I 137 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.587A pdb=" N PHE A 41 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 43 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 20 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.311A pdb=" N LEU A 94 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 669 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 96 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 666 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN A 145 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A 455 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE A 147 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 226 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AA7, first strand: chain 'A' and resid 707 through 710 removed outlier: 3.588A pdb=" N SER A 707 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1168 through 1174 removed outlier: 5.751A pdb=" N TRP A1192 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A1207 " --> pdb=" O TRP A1192 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A1194 " --> pdb=" O GLN A1205 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN A1205 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS A1196 " --> pdb=" O ALA A1203 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP A1201 " --> pdb=" O ASP A1198 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1965 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: 1.64 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2139 1.31 - 1.44: 2999 1.44 - 1.56: 6802 1.56 - 1.69: 3 1.69 - 1.81: 112 Bond restraints: 12055 Sorted by residual: bond pdb=" CA ILE A1244 " pdb=" C ILE A1244 " ideal model delta sigma weight residual 1.526 1.415 0.111 1.16e-02 7.43e+03 9.11e+01 bond pdb=" CA MET A1224 " pdb=" C MET A1224 " ideal model delta sigma weight residual 1.523 1.430 0.093 1.34e-02 5.57e+03 4.85e+01 bond pdb=" CA GLU A 152 " pdb=" C GLU A 152 " ideal model delta sigma weight residual 1.528 1.435 0.092 1.33e-02 5.65e+03 4.83e+01 bond pdb=" CA LYS A1221 " pdb=" C LYS A1221 " ideal model delta sigma weight residual 1.530 1.469 0.060 9.10e-03 1.21e+04 4.41e+01 bond pdb=" CA GLU A1104 " pdb=" C GLU A1104 " ideal model delta sigma weight residual 1.524 1.441 0.083 1.29e-02 6.01e+03 4.16e+01 ... (remaining 12050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 16020 3.82 - 7.65: 148 7.65 - 11.47: 13 11.47 - 15.29: 1 15.29 - 19.12: 2 Bond angle restraints: 16184 Sorted by residual: angle pdb=" N ILE A1089 " pdb=" CA ILE A1089 " pdb=" C ILE A1089 " ideal model delta sigma weight residual 113.53 94.41 19.12 9.80e-01 1.04e+00 3.81e+02 angle pdb=" N LYS A1221 " pdb=" CA LYS A1221 " pdb=" C LYS A1221 " ideal model delta sigma weight residual 108.49 89.98 18.51 1.15e+00 7.56e-01 2.59e+02 angle pdb=" N ARG A1102 " pdb=" CA ARG A1102 " pdb=" C ARG A1102 " ideal model delta sigma weight residual 111.82 101.33 10.49 1.16e+00 7.43e-01 8.17e+01 angle pdb=" N GLU I 105 " pdb=" CA GLU I 105 " pdb=" C GLU I 105 " ideal model delta sigma weight residual 111.36 102.39 8.97 1.09e+00 8.42e-01 6.77e+01 angle pdb=" N PHE A1249 " pdb=" CA PHE A1249 " pdb=" C PHE A1249 " ideal model delta sigma weight residual 111.14 102.90 8.24 1.08e+00 8.57e-01 5.82e+01 ... (remaining 16179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.25: 7170 31.25 - 62.51: 247 62.51 - 93.76: 15 93.76 - 125.01: 0 125.01 - 156.27: 3 Dihedral angle restraints: 7435 sinusoidal: 3188 harmonic: 4247 Sorted by residual: dihedral pdb=" N GLU A1103 " pdb=" C GLU A1103 " pdb=" CA GLU A1103 " pdb=" CB GLU A1103 " ideal model delta harmonic sigma weight residual 122.80 140.00 -17.20 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 96.27 -156.27 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" C GLU A1103 " pdb=" N GLU A1103 " pdb=" CA GLU A1103 " pdb=" CB GLU A1103 " ideal model delta harmonic sigma weight residual -122.60 -138.75 16.15 0 2.50e+00 1.60e-01 4.18e+01 ... (remaining 7432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1685 0.145 - 0.289: 33 0.289 - 0.434: 7 0.434 - 0.579: 0 0.579 - 0.724: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA GLU A1103 " pdb=" N GLU A1103 " pdb=" C GLU A1103 " pdb=" CB GLU A1103 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ILE A1244 " pdb=" N ILE A1244 " pdb=" C ILE A1244 " pdb=" CB ILE A1244 " both_signs ideal model delta sigma weight residual False 2.43 2.04 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA GLU A1254 " pdb=" N GLU A1254 " pdb=" C GLU A1254 " pdb=" CB GLU A1254 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1723 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 705 " -0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 706 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 706 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 706 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1082 " -0.033 2.00e-02 2.50e+03 2.08e-02 8.66e+00 pdb=" CG TYR A1082 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A1082 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A1082 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1082 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A1082 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1082 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A1082 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1212 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A1213 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " 0.035 5.00e-02 4.00e+02 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 129 2.51 - 3.11: 9509 3.11 - 3.71: 19529 3.71 - 4.30: 26689 4.30 - 4.90: 42974 Nonbonded interactions: 98830 Sorted by model distance: nonbonded pdb=" O1B ADP A2001 " pdb="MG MG A2002 " model vdw 1.918 2.170 nonbonded pdb="MG MG A2002 " pdb=" O2 PO4 A2003 " model vdw 1.976 2.170 nonbonded pdb=" OG SER A 204 " pdb="MG MG A2002 " model vdw 2.008 2.170 nonbonded pdb=" N LYS A1221 " pdb=" O LYS A1221 " model vdw 2.105 2.496 nonbonded pdb=" O LEU A1231 " pdb=" OG1 THR A1234 " model vdw 2.127 3.040 ... (remaining 98825 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 3 through 148) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.300 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 : 0.008 0.111 12055 Z= 0.467 Angle : 0.912 19.118 16184 Z= 0.565 Chirality : 0.060 0.724 1726 Planarity : 0.005 0.096 2127 Dihedral : 15.405 156.268 4677 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.63 % Allowed : 1.32 % Favored : 97.05 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.21), residues: 1441 helix: -0.00 (0.17), residues: 837 sheet: -2.39 (0.47), residues: 107 loop : -1.32 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 387 TYR 0.047 0.002 TYR A1082 PHE 0.039 0.003 PHE I 66 TRP 0.028 0.003 TRP A1253 HIS 0.009 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.47 (12055) covalent geometry : angle 0.91226 / 0.57 (16184) hydrogen bonds : bond 0.15433 / 10.27 ( 670) hydrogen bonds : angle 6.75064 / 4.89 ( 1965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 311 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6807 (pmm) cc_final: 0.6389 (pmm) REVERT: B 83 GLU cc_start: 0.7060 (tp30) cc_final: 0.6598 (tp30) REVERT: I 38 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6616 (ttm110) REVERT: I 42 GLN cc_start: 0.5856 (pp30) cc_final: 0.5120 (pp30) REVERT: I 50 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6981 (tm-30) REVERT: I 72 MET cc_start: 0.7568 (mmp) cc_final: 0.7363 (mmp) REVERT: I 73 MET cc_start: 0.7331 (tpt) cc_final: 0.6782 (tpt) REVERT: I 108 HIS cc_start: 0.7393 (m170) cc_final: 0.7191 (m170) REVERT: I 124 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7247 (mm-30) REVERT: I 141 GLU cc_start: 0.4240 (mm-30) cc_final: 0.3843 (mm-30) REVERT: A 5 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8251 (ptpp) REVERT: A 46 ASN cc_start: 0.7613 (p0) cc_final: 0.7408 (p0) REVERT: A 132 ASP cc_start: 0.6276 (t70) cc_final: 0.5794 (t0) REVERT: A 135 PHE cc_start: 0.7674 (t80) cc_final: 0.7359 (t80) REVERT: A 138 MET cc_start: 0.7230 (tmm) cc_final: 0.6971 (tmm) REVERT: A 176 GLN cc_start: 0.7550 (pm20) cc_final: 0.7230 (pm20) REVERT: A 180 ASP cc_start: 0.7356 (m-30) cc_final: 0.7017 (m-30) REVERT: A 196 LYS cc_start: 0.8249 (tttm) cc_final: 0.7905 (tttm) REVERT: A 264 HIS cc_start: 0.7727 (m170) cc_final: 0.7376 (m170) REVERT: A 327 ILE cc_start: 0.7967 (pt) cc_final: 0.7226 (pt) REVERT: A 377 GLU cc_start: 0.7785 (tt0) cc_final: 0.7583 (tt0) REVERT: A 387 ARG cc_start: 0.7443 (pmt170) cc_final: 0.6936 (pmt170) REVERT: A 491 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 575 GLU cc_start: 0.6286 (mp0) cc_final: 0.6029 (mp0) REVERT: A 596 LYS cc_start: 0.8142 (mptt) cc_final: 0.7883 (mptt) REVERT: A 609 ILE cc_start: 0.8229 (tp) cc_final: 0.7966 (tp) REVERT: A 611 GLU cc_start: 0.6973 (mp0) cc_final: 0.6766 (mp0) REVERT: A 617 ILE cc_start: 0.8336 (mm) cc_final: 0.8065 (mm) REVERT: A 619 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6555 (mt-10) REVERT: A 701 MET cc_start: 0.7078 (mmt) cc_final: 0.6789 (mmt) REVERT: A 732 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7778 (ttp80) REVERT: A 765 GLU cc_start: 0.6707 (mp0) cc_final: 0.6396 (mp0) REVERT: A 799 CYS cc_start: 0.6902 (t) cc_final: 0.6629 (t) REVERT: A 802 SER cc_start: 0.7427 (t) cc_final: 0.7073 (p) REVERT: A 956 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7416 (tmm) REVERT: A 959 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: A 961 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: A 1104 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 1105 PHE cc_start: 0.8186 (t80) cc_final: 0.7926 (t80) REVERT: A 1193 TRP cc_start: 0.8375 (t60) cc_final: 0.8087 (t60) REVERT: A 1223 ASP cc_start: 0.7276 (t0) cc_final: 0.6716 (t0) outliers start: 21 outliers final: 5 residues processed: 323 average time/residue: 0.1098 time to fit residues: 48.7474 Evaluate side-chains 305 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 297 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 MET Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1222 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN A 511 ASN A 868 ASN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138814 restraints weight = 19281.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143443 restraints weight = 9044.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146437 restraints weight = 5318.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.148140 restraints weight = 3650.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.149564 restraints weight = 2859.740| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12055 Z= 0.149 Angle : 0.643 10.200 16184 Z= 0.338 Chirality : 0.043 0.165 1726 Planarity : 0.005 0.063 2127 Dihedral : 8.857 154.314 1611 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 8.84 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1441 helix: 0.64 (0.17), residues: 851 sheet: -1.87 (0.48), residues: 112 loop : -1.06 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 87 TYR 0.013 0.002 TYR A 300 PHE 0.037 0.002 PHE A 853 TRP 0.040 0.002 TRP A1253 HIS 0.003 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (12055) covalent geometry : angle 0.64283 / 0.34 (16184) hydrogen bonds : bond 0.04545 / 3.01 ( 670) hydrogen bonds : angle 4.91693 / 3.55 ( 1965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 305 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8250 (mtp) cc_final: 0.7864 (mtm) REVERT: B 73 MET cc_start: 0.6547 (mmt) cc_final: 0.6198 (mmp) REVERT: B 77 MET cc_start: 0.6675 (pmm) cc_final: 0.6293 (pmm) REVERT: B 83 GLU cc_start: 0.6856 (tp30) cc_final: 0.6462 (tp30) REVERT: I 12 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7536 (tm-30) REVERT: I 50 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7201 (tm-30) REVERT: I 73 MET cc_start: 0.7211 (tpt) cc_final: 0.5781 (tpt) REVERT: I 77 MET cc_start: 0.7628 (ptp) cc_final: 0.6389 (ptp) REVERT: I 107 ARG cc_start: 0.7418 (ttt-90) cc_final: 0.7108 (ttt-90) REVERT: I 108 HIS cc_start: 0.7323 (m170) cc_final: 0.7050 (m170) REVERT: I 110 MET cc_start: 0.7128 (mpp) cc_final: 0.6922 (mpp) REVERT: I 120 GLU cc_start: 0.7385 (pm20) cc_final: 0.7059 (pm20) REVERT: I 146 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6331 (mmm) REVERT: A 24 ILE cc_start: 0.7809 (mt) cc_final: 0.7548 (mt) REVERT: A 56 LYS cc_start: 0.8212 (mppt) cc_final: 0.7773 (mppt) REVERT: A 125 PRO cc_start: 0.8378 (Cg_exo) cc_final: 0.8141 (Cg_endo) REVERT: A 132 ASP cc_start: 0.6322 (t70) cc_final: 0.6114 (t0) REVERT: A 146 SER cc_start: 0.8114 (p) cc_final: 0.7820 (m) REVERT: A 197 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7737 (p) REVERT: A 228 TYR cc_start: 0.8498 (m-80) cc_final: 0.7891 (m-80) REVERT: A 232 LYS cc_start: 0.7903 (mttp) cc_final: 0.7644 (mttp) REVERT: A 264 HIS cc_start: 0.7656 (m170) cc_final: 0.7375 (m170) REVERT: A 316 ASP cc_start: 0.6648 (m-30) cc_final: 0.5964 (m-30) REVERT: A 327 ILE cc_start: 0.8023 (pt) cc_final: 0.7731 (pt) REVERT: A 377 GLU cc_start: 0.7734 (tt0) cc_final: 0.7493 (tt0) REVERT: A 448 SER cc_start: 0.8290 (p) cc_final: 0.8016 (m) REVERT: A 575 GLU cc_start: 0.6202 (mp0) cc_final: 0.5814 (mp0) REVERT: A 580 ARG cc_start: 0.6756 (mpp80) cc_final: 0.6193 (mpp80) REVERT: A 603 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6828 (tpt) REVERT: A 619 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6549 (mt-10) REVERT: A 701 MET cc_start: 0.7127 (mmt) cc_final: 0.6855 (mmt) REVERT: A 732 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7141 (ttp80) REVERT: A 736 LYS cc_start: 0.7886 (tppt) cc_final: 0.7518 (ttmm) REVERT: A 765 GLU cc_start: 0.6774 (mp0) cc_final: 0.6419 (mp0) REVERT: A 848 LYS cc_start: 0.7294 (mmtm) cc_final: 0.7070 (mmtm) REVERT: A 870 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7446 (pp30) REVERT: A 956 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7054 (ttp) REVERT: A 959 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: A 961 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: A 1091 THR cc_start: 0.7153 (OUTLIER) cc_final: 0.6551 (t) REVERT: A 1104 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 1105 PHE cc_start: 0.8103 (t80) cc_final: 0.7804 (t80) REVERT: A 1222 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.6419 (m-30) outliers start: 25 outliers final: 6 residues processed: 315 average time/residue: 0.1000 time to fit residues: 43.8316 Evaluate side-chains 308 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 294 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 956 MET Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1227 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 11 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN A 919 GLN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** 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 = 0.4070 r_free = 0.4070 target = 0.160566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137259 restraints weight = 19376.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141956 restraints weight = 9146.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144972 restraints weight = 5418.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.146975 restraints weight = 3735.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.148101 restraints weight = 2854.020| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12055 Z= 0.199 Angle : 0.623 9.090 16184 Z= 0.331 Chirality : 0.042 0.182 1726 Planarity : 0.004 0.050 2127 Dihedral : 8.312 155.074 1604 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.18 % Rotamer: Outliers : 2.33 % Allowed : 12.71 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1441 helix: 0.79 (0.17), residues: 854 sheet: -1.92 (0.47), residues: 115 loop : -1.02 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 87 TYR 0.014 0.002 TYR A1082 PHE 0.025 0.002 PHE I 90 TRP 0.026 0.002 TRP A1253 HIS 0.007 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (12055) covalent geometry : angle 0.62290 / 0.33 (16184) hydrogen bonds : bond 0.04585 / 3.01 ( 670) hydrogen bonds : angle 4.88605 / 3.52 ( 1965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6573 (mmt) cc_final: 0.6174 (mmt) REVERT: B 77 MET cc_start: 0.6691 (pmm) cc_final: 0.6312 (pmm) REVERT: B 83 GLU cc_start: 0.6915 (tp30) cc_final: 0.6537 (tp30) REVERT: B 128 GLU cc_start: 0.6606 (tm-30) cc_final: 0.6347 (tm-30) REVERT: I 12 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7617 (tm-30) REVERT: I 38 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6898 (ttm110) REVERT: I 50 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7301 (tm-30) REVERT: I 73 MET cc_start: 0.7186 (tpt) cc_final: 0.5894 (tpt) REVERT: I 77 MET cc_start: 0.7630 (ptp) cc_final: 0.6523 (ptp) REVERT: I 107 ARG cc_start: 0.7399 (ttt-90) cc_final: 0.7037 (ttt-90) REVERT: I 108 HIS cc_start: 0.7270 (m170) cc_final: 0.7017 (m170) REVERT: I 146 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6224 (mmm) REVERT: A 24 ILE cc_start: 0.7863 (mt) cc_final: 0.7595 (mt) REVERT: A 56 LYS cc_start: 0.8208 (mppt) cc_final: 0.7781 (mppt) REVERT: A 132 ASP cc_start: 0.6363 (t70) cc_final: 0.6068 (t0) REVERT: A 138 MET cc_start: 0.7358 (tmm) cc_final: 0.7127 (ttp) REVERT: A 264 HIS cc_start: 0.7657 (m170) cc_final: 0.7370 (m170) REVERT: A 316 ASP cc_start: 0.6608 (m-30) cc_final: 0.5885 (m-30) REVERT: A 327 ILE cc_start: 0.8108 (pt) cc_final: 0.7891 (pt) REVERT: A 377 GLU cc_start: 0.7777 (tt0) cc_final: 0.7522 (tt0) REVERT: A 415 GLN cc_start: 0.7884 (mt0) cc_final: 0.7131 (mp10) REVERT: A 448 SER cc_start: 0.8227 (p) cc_final: 0.7979 (m) REVERT: A 491 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 580 ARG cc_start: 0.7010 (mpp80) cc_final: 0.6355 (mpp80) REVERT: A 603 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6803 (tpt) REVERT: A 619 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6582 (mt-10) REVERT: A 732 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7749 (ttp80) REVERT: A 733 LEU cc_start: 0.8342 (mt) cc_final: 0.8016 (mt) REVERT: A 765 GLU cc_start: 0.6806 (mp0) cc_final: 0.6440 (mp0) REVERT: A 848 LYS cc_start: 0.7385 (mmtm) cc_final: 0.7144 (mmtm) REVERT: A 959 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: A 960 MET cc_start: 0.7819 (mmm) cc_final: 0.7247 (mmm) REVERT: A 1104 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6794 (mm-30) REVERT: A 1105 PHE cc_start: 0.8039 (t80) cc_final: 0.7828 (t80) REVERT: A 1171 PHE cc_start: 0.7961 (m-80) cc_final: 0.7690 (m-10) REVERT: A 1221 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7325 (mttt) outliers start: 30 outliers final: 13 residues processed: 301 average time/residue: 0.1103 time to fit residues: 45.9285 Evaluate side-chains 300 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 283 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 873 ASN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** 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 = 0.4061 r_free = 0.4061 target = 0.159452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136058 restraints weight = 19367.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140719 restraints weight = 9204.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.143705 restraints weight = 5449.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.145688 restraints weight = 3761.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146732 restraints weight = 2888.111| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12055 Z= 0.226 Angle : 0.636 10.945 16184 Z= 0.334 Chirality : 0.043 0.193 1726 Planarity : 0.004 0.052 2127 Dihedral : 8.081 160.626 1595 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 2.56 % Allowed : 13.95 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1441 helix: 0.82 (0.17), residues: 853 sheet: -2.00 (0.47), residues: 115 loop : -1.10 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 87 TYR 0.014 0.002 TYR A 812 PHE 0.041 0.003 PHE A 853 TRP 0.023 0.002 TRP A1253 HIS 0.008 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (12055) covalent geometry : angle 0.63638 / 0.33 (16184) hydrogen bonds : bond 0.04565 / 3.01 ( 670) hydrogen bonds : angle 4.88176 / 3.52 ( 1965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6626 (mmt) cc_final: 0.6204 (mmt) REVERT: B 77 MET cc_start: 0.6684 (pmm) cc_final: 0.6278 (pmm) REVERT: B 83 GLU cc_start: 0.6961 (tp30) cc_final: 0.6536 (tp30) REVERT: I 12 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7516 (tm-30) REVERT: I 38 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.6700 (ttm110) REVERT: I 50 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7358 (tm-30) REVERT: I 70 LEU cc_start: 0.8384 (tt) cc_final: 0.8142 (tt) REVERT: I 73 MET cc_start: 0.7130 (tpt) cc_final: 0.5923 (tpt) REVERT: I 77 MET cc_start: 0.7626 (ptp) cc_final: 0.6638 (ptp) REVERT: I 92 VAL cc_start: 0.8387 (t) cc_final: 0.8180 (t) REVERT: I 107 ARG cc_start: 0.7382 (ttt-90) cc_final: 0.7149 (ttt-90) REVERT: I 108 HIS cc_start: 0.7257 (m170) cc_final: 0.7017 (m170) REVERT: I 146 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6706 (mtm) REVERT: A 24 ILE cc_start: 0.7863 (mt) cc_final: 0.7578 (mt) REVERT: A 56 LYS cc_start: 0.8221 (mppt) cc_final: 0.7779 (mppt) REVERT: A 61 ASP cc_start: 0.7121 (t70) cc_final: 0.6716 (t0) REVERT: A 132 ASP cc_start: 0.6419 (t70) cc_final: 0.6156 (t70) REVERT: A 137 ASP cc_start: 0.7245 (m-30) cc_final: 0.6554 (m-30) REVERT: A 231 GLU cc_start: 0.6773 (tt0) cc_final: 0.6515 (tt0) REVERT: A 232 LYS cc_start: 0.7980 (mttp) cc_final: 0.7725 (mttp) REVERT: A 264 HIS cc_start: 0.7680 (m170) cc_final: 0.7427 (m170) REVERT: A 377 GLU cc_start: 0.7774 (tt0) cc_final: 0.7534 (tt0) REVERT: A 448 SER cc_start: 0.8260 (p) cc_final: 0.8009 (m) REVERT: A 603 MET cc_start: 0.7309 (tpt) cc_final: 0.6802 (tpt) REVERT: A 619 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6594 (mt-10) REVERT: A 701 MET cc_start: 0.7086 (mmt) cc_final: 0.6877 (mmt) REVERT: A 732 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7498 (ttp80) REVERT: A 736 LYS cc_start: 0.7979 (tppt) cc_final: 0.7730 (ttmm) REVERT: A 765 GLU cc_start: 0.6791 (mp0) cc_final: 0.6464 (mp0) REVERT: A 848 LYS cc_start: 0.7399 (mmtm) cc_final: 0.7183 (mmtm) REVERT: A 872 LYS cc_start: 0.8646 (mttp) cc_final: 0.8253 (mptp) REVERT: A 956 MET cc_start: 0.7746 (tpp) cc_final: 0.7178 (tpp) REVERT: A 959 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: A 1104 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 1221 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7164 (mttt) outliers start: 33 outliers final: 22 residues processed: 304 average time/residue: 0.1163 time to fit residues: 48.6462 Evaluate side-chains 309 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.160046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136706 restraints weight = 19408.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141382 restraints weight = 9148.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144399 restraints weight = 5396.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.146372 restraints weight = 3707.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.147618 restraints weight = 2842.014| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12055 Z= 0.194 Angle : 0.621 9.005 16184 Z= 0.326 Chirality : 0.042 0.184 1726 Planarity : 0.004 0.054 2127 Dihedral : 8.037 170.095 1595 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.79 % Allowed : 15.50 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1441 helix: 0.96 (0.17), residues: 853 sheet: -1.94 (0.47), residues: 115 loop : -1.02 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 87 TYR 0.014 0.002 TYR A1082 PHE 0.041 0.003 PHE A 853 TRP 0.022 0.002 TRP A1253 HIS 0.006 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (12055) covalent geometry : angle 0.62112 / 0.33 (16184) hydrogen bonds : bond 0.04355 / 2.87 ( 670) hydrogen bonds : angle 4.79448 / 3.46 ( 1965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6641 (pmm) cc_final: 0.6262 (pmm) REVERT: B 83 GLU cc_start: 0.6868 (tp30) cc_final: 0.6473 (tp30) REVERT: I 12 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7594 (tm-30) REVERT: I 38 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.6738 (ttm110) REVERT: I 42 GLN cc_start: 0.5803 (pp30) cc_final: 0.5224 (pp30) REVERT: I 50 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7358 (tm-30) REVERT: I 70 LEU cc_start: 0.8368 (tt) cc_final: 0.8111 (tt) REVERT: I 72 MET cc_start: 0.6682 (mmt) cc_final: 0.6187 (mmt) REVERT: I 73 MET cc_start: 0.7071 (tpt) cc_final: 0.6000 (tpt) REVERT: I 77 MET cc_start: 0.7620 (ptp) cc_final: 0.6608 (ptp) REVERT: I 92 VAL cc_start: 0.8389 (t) cc_final: 0.8184 (t) REVERT: I 107 ARG cc_start: 0.7387 (ttt-90) cc_final: 0.7118 (ttt-90) REVERT: I 108 HIS cc_start: 0.7262 (m170) cc_final: 0.7034 (m170) REVERT: I 146 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6452 (mmm) REVERT: A 24 ILE cc_start: 0.7874 (mt) cc_final: 0.7611 (mt) REVERT: A 56 LYS cc_start: 0.8220 (mppt) cc_final: 0.7773 (mppt) REVERT: A 57 LYS cc_start: 0.7364 (mtmt) cc_final: 0.7105 (mtmm) REVERT: A 61 ASP cc_start: 0.7130 (t70) cc_final: 0.6720 (t0) REVERT: A 132 ASP cc_start: 0.6389 (t70) cc_final: 0.5892 (t0) REVERT: A 232 LYS cc_start: 0.7968 (mttp) cc_final: 0.7735 (mttp) REVERT: A 264 HIS cc_start: 0.7670 (m170) cc_final: 0.7432 (m170) REVERT: A 319 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.6937 (mtm-85) REVERT: A 377 GLU cc_start: 0.7772 (tt0) cc_final: 0.7536 (tt0) REVERT: A 415 GLN cc_start: 0.7927 (mt0) cc_final: 0.7124 (pm20) REVERT: A 448 SER cc_start: 0.8274 (p) cc_final: 0.8038 (m) REVERT: A 603 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6798 (tpt) REVERT: A 701 MET cc_start: 0.7103 (mmt) cc_final: 0.6763 (mmt) REVERT: A 732 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7111 (ttp80) REVERT: A 736 LYS cc_start: 0.7937 (tppt) cc_final: 0.7433 (ttmm) REVERT: A 765 GLU cc_start: 0.6804 (mp0) cc_final: 0.6457 (mp0) REVERT: A 848 LYS cc_start: 0.7423 (mmtm) cc_final: 0.7185 (mmtm) REVERT: A 872 LYS cc_start: 0.8673 (mttp) cc_final: 0.8279 (mptp) REVERT: A 956 MET cc_start: 0.7682 (tpp) cc_final: 0.7408 (tpp) REVERT: A 959 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: A 1084 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7191 (tp30) REVERT: A 1104 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6874 (mm-30) REVERT: A 1221 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7106 (mttt) outliers start: 36 outliers final: 18 residues processed: 302 average time/residue: 0.1139 time to fit residues: 47.5160 Evaluate side-chains 310 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 78 optimal weight: 0.0770 chunk 139 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 121 optimal weight: 0.1980 chunk 29 optimal weight: 0.0770 overall best weight: 0.1474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.163442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140094 restraints weight = 19383.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144861 restraints weight = 9152.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147878 restraints weight = 5362.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.149897 restraints weight = 3674.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.150990 restraints weight = 2800.933| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12055 Z= 0.114 Angle : 0.591 9.868 16184 Z= 0.302 Chirality : 0.040 0.179 1726 Planarity : 0.004 0.049 2127 Dihedral : 7.737 179.334 1595 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.36 % Rotamer: Outliers : 2.33 % Allowed : 17.05 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1441 helix: 1.42 (0.17), residues: 851 sheet: -1.44 (0.52), residues: 102 loop : -0.79 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 87 TYR 0.012 0.001 TYR A1082 PHE 0.037 0.002 PHE I 66 TRP 0.022 0.001 TRP A1253 HIS 0.003 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (12055) covalent geometry : angle 0.59053 / 0.30 (16184) hydrogen bonds : bond 0.03675 / 2.41 ( 670) hydrogen bonds : angle 4.45234 / 3.21 ( 1965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6547 (pmm) cc_final: 0.6168 (pmm) REVERT: B 83 GLU cc_start: 0.6846 (tp30) cc_final: 0.6446 (tp30) REVERT: I 12 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7631 (tm-30) REVERT: I 38 ARG cc_start: 0.6793 (ttm-80) cc_final: 0.6459 (ttm110) REVERT: I 50 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7310 (tm-30) REVERT: I 70 LEU cc_start: 0.8325 (tt) cc_final: 0.8063 (tt) REVERT: I 73 MET cc_start: 0.7212 (tpt) cc_final: 0.6068 (tpt) REVERT: I 77 MET cc_start: 0.7636 (ptp) cc_final: 0.6702 (ptp) REVERT: I 107 ARG cc_start: 0.7392 (ttt-90) cc_final: 0.7105 (ttt-90) REVERT: I 108 HIS cc_start: 0.7293 (m170) cc_final: 0.7065 (m170) REVERT: I 110 MET cc_start: 0.7190 (mpp) cc_final: 0.6941 (mpp) REVERT: I 146 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.5995 (mmm) REVERT: A 16 PHE cc_start: 0.8075 (m-80) cc_final: 0.7446 (m-80) REVERT: A 24 ILE cc_start: 0.7857 (mt) cc_final: 0.7648 (mt) REVERT: A 56 LYS cc_start: 0.8231 (mppt) cc_final: 0.7806 (mppt) REVERT: A 60 GLU cc_start: 0.6252 (mt-10) cc_final: 0.5996 (mt-10) REVERT: A 61 ASP cc_start: 0.7123 (t70) cc_final: 0.6690 (t0) REVERT: A 132 ASP cc_start: 0.6367 (t70) cc_final: 0.6071 (t0) REVERT: A 171 SER cc_start: 0.8369 (t) cc_final: 0.7825 (p) REVERT: A 231 GLU cc_start: 0.6936 (tt0) cc_final: 0.6683 (tt0) REVERT: A 264 HIS cc_start: 0.7541 (m170) cc_final: 0.7272 (m170) REVERT: A 319 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.6954 (mtt-85) REVERT: A 377 GLU cc_start: 0.7745 (tt0) cc_final: 0.7429 (tt0) REVERT: A 415 GLN cc_start: 0.7919 (mt0) cc_final: 0.7166 (mp10) REVERT: A 448 SER cc_start: 0.8229 (p) cc_final: 0.7981 (m) REVERT: A 468 PHE cc_start: 0.7182 (t80) cc_final: 0.6976 (t80) REVERT: A 596 LYS cc_start: 0.8122 (mptt) cc_final: 0.7654 (mmtp) REVERT: A 603 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6736 (tpt) REVERT: A 701 MET cc_start: 0.7079 (mmt) cc_final: 0.6750 (mmt) REVERT: A 732 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7125 (ttp80) REVERT: A 736 LYS cc_start: 0.7729 (tppt) cc_final: 0.7198 (ttmm) REVERT: A 765 GLU cc_start: 0.6795 (mp0) cc_final: 0.6505 (mp0) REVERT: A 848 LYS cc_start: 0.7397 (mmtm) cc_final: 0.7132 (mmtm) REVERT: A 872 LYS cc_start: 0.8668 (mttp) cc_final: 0.8242 (mptp) REVERT: A 956 MET cc_start: 0.7673 (tpp) cc_final: 0.7267 (tpp) REVERT: A 959 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: A 1221 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6812 (mttt) outliers start: 30 outliers final: 15 residues processed: 299 average time/residue: 0.1131 time to fit residues: 46.5352 Evaluate side-chains 288 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 269 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1221 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.160046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136919 restraints weight = 19275.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141523 restraints weight = 9087.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144550 restraints weight = 5375.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146366 restraints weight = 3694.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147829 restraints weight = 2858.940| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12055 Z= 0.205 Angle : 0.658 10.796 16184 Z= 0.341 Chirality : 0.043 0.171 1726 Planarity : 0.004 0.050 2127 Dihedral : 7.715 167.958 1595 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 3.02 % Allowed : 17.67 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1441 helix: 1.21 (0.17), residues: 851 sheet: -1.56 (0.50), residues: 111 loop : -0.81 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 87 TYR 0.025 0.002 TYR A 462 PHE 0.034 0.003 PHE A1105 TRP 0.021 0.002 TRP A1253 HIS 0.007 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (12055) covalent geometry : angle 0.65777 / 0.34 (16184) hydrogen bonds : bond 0.04263 / 2.81 ( 670) hydrogen bonds : angle 4.68045 / 3.37 ( 1965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 GLU cc_start: 0.6930 (tp30) cc_final: 0.6706 (tp30) REVERT: B 77 MET cc_start: 0.6608 (pmm) cc_final: 0.6224 (pmm) REVERT: B 83 GLU cc_start: 0.6944 (tp30) cc_final: 0.6557 (tp30) REVERT: I 38 ARG cc_start: 0.7022 (ttm-80) cc_final: 0.6704 (ttm110) REVERT: I 50 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7381 (tm-30) REVERT: I 70 LEU cc_start: 0.8365 (tt) cc_final: 0.8099 (tt) REVERT: I 73 MET cc_start: 0.6937 (tpt) cc_final: 0.5965 (tpt) REVERT: I 77 MET cc_start: 0.7615 (ptp) cc_final: 0.6680 (ptp) REVERT: I 101 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6355 (mm) REVERT: I 107 ARG cc_start: 0.7324 (ttt-90) cc_final: 0.7037 (ttt-90) REVERT: I 108 HIS cc_start: 0.7301 (m170) cc_final: 0.7043 (m170) REVERT: I 146 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6548 (mtm) REVERT: A 23 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.6937 (t70) REVERT: A 24 ILE cc_start: 0.7827 (mt) cc_final: 0.7410 (mt) REVERT: A 56 LYS cc_start: 0.8261 (mppt) cc_final: 0.7954 (mmtm) REVERT: A 61 ASP cc_start: 0.7131 (t70) cc_final: 0.6750 (t0) REVERT: A 132 ASP cc_start: 0.6412 (t70) cc_final: 0.6035 (t0) REVERT: A 137 ASP cc_start: 0.7241 (m-30) cc_final: 0.6548 (m-30) REVERT: A 231 GLU cc_start: 0.6886 (tt0) cc_final: 0.6634 (tt0) REVERT: A 264 HIS cc_start: 0.7620 (m170) cc_final: 0.7333 (m170) REVERT: A 377 GLU cc_start: 0.7741 (tt0) cc_final: 0.7460 (tt0) REVERT: A 448 SER cc_start: 0.8257 (p) cc_final: 0.8030 (m) REVERT: A 603 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6945 (tpt) REVERT: A 701 MET cc_start: 0.7135 (mmt) cc_final: 0.6728 (mmt) REVERT: A 732 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7805 (ttp80) REVERT: A 765 GLU cc_start: 0.6808 (mp0) cc_final: 0.6387 (mp0) REVERT: A 848 LYS cc_start: 0.7418 (mmtm) cc_final: 0.7170 (mmtm) REVERT: A 872 LYS cc_start: 0.8680 (mttp) cc_final: 0.8236 (mptp) REVERT: A 956 MET cc_start: 0.7674 (tpp) cc_final: 0.7428 (tpp) REVERT: A 959 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: A 1104 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6995 (mm-30) REVERT: A 1221 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6996 (mttt) outliers start: 39 outliers final: 19 residues processed: 298 average time/residue: 0.1097 time to fit residues: 45.1899 Evaluate side-chains 301 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1221 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 133 optimal weight: 0.0970 chunk 19 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 99 optimal weight: 0.0870 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.161412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138159 restraints weight = 19347.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142858 restraints weight = 9196.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145920 restraints weight = 5441.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147889 restraints weight = 3731.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.149128 restraints weight = 2854.761| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12055 Z= 0.140 Angle : 0.631 10.800 16184 Z= 0.323 Chirality : 0.041 0.261 1726 Planarity : 0.004 0.050 2127 Dihedral : 7.506 163.223 1595 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 2.56 % Allowed : 18.29 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1441 helix: 1.36 (0.17), residues: 854 sheet: -1.46 (0.50), residues: 110 loop : -0.72 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 87 TYR 0.021 0.001 TYR A 462 PHE 0.035 0.002 PHE I 66 TRP 0.022 0.001 TRP A1253 HIS 0.004 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12055) covalent geometry : angle 0.63122 / 0.32 (16184) hydrogen bonds : bond 0.03852 / 2.54 ( 670) hydrogen bonds : angle 4.51241 / 3.25 ( 1965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6566 (pmm) cc_final: 0.6177 (pmm) REVERT: B 83 GLU cc_start: 0.6830 (tp30) cc_final: 0.6460 (tp30) REVERT: I 38 ARG cc_start: 0.6820 (ttm-80) cc_final: 0.6523 (ttm110) REVERT: I 50 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7345 (tm-30) REVERT: I 70 LEU cc_start: 0.8336 (tt) cc_final: 0.8072 (tt) REVERT: I 73 MET cc_start: 0.6905 (tpt) cc_final: 0.5901 (tpt) REVERT: I 77 MET cc_start: 0.7591 (ptp) cc_final: 0.6604 (ptp) REVERT: I 107 ARG cc_start: 0.7395 (ttt-90) cc_final: 0.7043 (ttt-90) REVERT: I 108 HIS cc_start: 0.7305 (m170) cc_final: 0.7067 (m170) REVERT: I 146 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6477 (mtm) REVERT: A 23 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.6819 (t70) REVERT: A 24 ILE cc_start: 0.7846 (mt) cc_final: 0.7419 (mt) REVERT: A 57 LYS cc_start: 0.7356 (mtmt) cc_final: 0.7046 (mtmt) REVERT: A 61 ASP cc_start: 0.7115 (t70) cc_final: 0.6690 (t0) REVERT: A 113 LYS cc_start: 0.7776 (ptpt) cc_final: 0.7531 (ptpt) REVERT: A 132 ASP cc_start: 0.6391 (t70) cc_final: 0.6057 (t0) REVERT: A 231 GLU cc_start: 0.6806 (tt0) cc_final: 0.6553 (tt0) REVERT: A 264 HIS cc_start: 0.7553 (m170) cc_final: 0.7271 (m170) REVERT: A 319 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: A 377 GLU cc_start: 0.7713 (tt0) cc_final: 0.7474 (tt0) REVERT: A 448 SER cc_start: 0.8208 (p) cc_final: 0.7969 (m) REVERT: A 603 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6848 (tpt) REVERT: A 701 MET cc_start: 0.7119 (mmt) cc_final: 0.6702 (mmt) REVERT: A 732 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7200 (ttp80) REVERT: A 736 LYS cc_start: 0.7840 (tppt) cc_final: 0.7261 (ttmm) REVERT: A 765 GLU cc_start: 0.6816 (mp0) cc_final: 0.6383 (mp0) REVERT: A 872 LYS cc_start: 0.8651 (mttp) cc_final: 0.8420 (mttp) REVERT: A 956 MET cc_start: 0.7662 (tpp) cc_final: 0.7423 (tpp) REVERT: A 959 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: A 1084 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: A 1089 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7525 (mm) REVERT: A 1104 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6906 (mm-30) REVERT: A 1221 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6869 (mttt) outliers start: 33 outliers final: 19 residues processed: 294 average time/residue: 0.1116 time to fit residues: 45.1315 Evaluate side-chains 301 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1221 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 0.0170 chunk 76 optimal weight: 0.0670 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.161200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137811 restraints weight = 19339.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142516 restraints weight = 9191.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145613 restraints weight = 5447.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147558 restraints weight = 3729.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148777 restraints weight = 2860.425| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12055 Z= 0.157 Angle : 0.649 10.625 16184 Z= 0.332 Chirality : 0.042 0.217 1726 Planarity : 0.004 0.050 2127 Dihedral : 7.346 154.283 1595 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 2.71 % Allowed : 18.99 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1441 helix: 1.35 (0.17), residues: 855 sheet: -1.52 (0.49), residues: 111 loop : -0.68 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 87 TYR 0.021 0.002 TYR A 462 PHE 0.033 0.002 PHE A1105 TRP 0.021 0.001 TRP A1253 HIS 0.005 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (12055) covalent geometry : angle 0.64901 / 0.33 (16184) hydrogen bonds : bond 0.03897 / 2.56 ( 670) hydrogen bonds : angle 4.50570 / 3.25 ( 1965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6577 (pmm) cc_final: 0.6176 (pmm) REVERT: B 83 GLU cc_start: 0.6879 (tp30) cc_final: 0.6497 (tp30) REVERT: I 38 ARG cc_start: 0.6843 (ttm-80) cc_final: 0.6586 (ttm110) REVERT: I 70 LEU cc_start: 0.8408 (tt) cc_final: 0.8141 (tt) REVERT: I 73 MET cc_start: 0.6913 (tpt) cc_final: 0.5926 (tpt) REVERT: I 77 MET cc_start: 0.7607 (ptp) cc_final: 0.6621 (ptp) REVERT: I 101 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6430 (mm) REVERT: I 107 ARG cc_start: 0.7431 (ttt-90) cc_final: 0.7108 (ttt-90) REVERT: I 108 HIS cc_start: 0.7315 (m170) cc_final: 0.7090 (m170) REVERT: I 110 MET cc_start: 0.7225 (mpp) cc_final: 0.6940 (mpp) REVERT: I 146 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6487 (mtm) REVERT: A 23 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.6849 (t70) REVERT: A 24 ILE cc_start: 0.7808 (mt) cc_final: 0.7396 (mt) REVERT: A 57 LYS cc_start: 0.7356 (mtmt) cc_final: 0.7074 (mtmm) REVERT: A 61 ASP cc_start: 0.7095 (t70) cc_final: 0.6716 (t0) REVERT: A 88 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7717 (t) REVERT: A 113 LYS cc_start: 0.7785 (ptpt) cc_final: 0.7576 (ptpt) REVERT: A 132 ASP cc_start: 0.6404 (t70) cc_final: 0.6064 (t0) REVERT: A 171 SER cc_start: 0.8400 (t) cc_final: 0.7857 (p) REVERT: A 231 GLU cc_start: 0.6815 (tt0) cc_final: 0.6560 (tt0) REVERT: A 264 HIS cc_start: 0.7569 (m170) cc_final: 0.7266 (m170) REVERT: A 319 ARG cc_start: 0.7617 (mtm-85) cc_final: 0.6946 (mtm-85) REVERT: A 387 ARG cc_start: 0.7775 (ptm160) cc_final: 0.7513 (ptm160) REVERT: A 448 SER cc_start: 0.8199 (p) cc_final: 0.7970 (m) REVERT: A 596 LYS cc_start: 0.8091 (mttm) cc_final: 0.7533 (mmtp) REVERT: A 603 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6766 (tpt) REVERT: A 701 MET cc_start: 0.7125 (mmt) cc_final: 0.6694 (mmt) REVERT: A 732 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7231 (ttp80) REVERT: A 736 LYS cc_start: 0.7864 (tppt) cc_final: 0.7281 (ttmm) REVERT: A 765 GLU cc_start: 0.6776 (mp0) cc_final: 0.6355 (mp0) REVERT: A 872 LYS cc_start: 0.8648 (mttp) cc_final: 0.8409 (mttp) REVERT: A 956 MET cc_start: 0.7671 (tpp) cc_final: 0.7442 (tpp) REVERT: A 959 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: A 1084 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: A 1089 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7549 (mm) REVERT: A 1104 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6927 (mm-30) REVERT: A 1202 ILE cc_start: 0.8033 (tp) cc_final: 0.7712 (tt) REVERT: A 1221 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6862 (mttt) outliers start: 35 outliers final: 22 residues processed: 293 average time/residue: 0.1037 time to fit residues: 42.3031 Evaluate side-chains 304 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1221 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** 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 = 0.4083 r_free = 0.4083 target = 0.160892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137483 restraints weight = 19386.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142202 restraints weight = 9237.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.145243 restraints weight = 5465.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147271 restraints weight = 3752.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148581 restraints weight = 2854.959| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12055 Z= 0.171 Angle : 0.665 11.240 16184 Z= 0.341 Chirality : 0.043 0.214 1726 Planarity : 0.004 0.050 2127 Dihedral : 7.170 142.225 1595 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 2.71 % Allowed : 19.38 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1441 helix: 1.30 (0.17), residues: 854 sheet: -1.57 (0.49), residues: 111 loop : -0.71 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 87 TYR 0.027 0.002 TYR A 718 PHE 0.033 0.003 PHE A1105 TRP 0.021 0.002 TRP A1253 HIS 0.005 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (12055) covalent geometry : angle 0.66470 / 0.34 (16184) hydrogen bonds : bond 0.03975 / 2.62 ( 670) hydrogen bonds : angle 4.54428 / 3.27 ( 1965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6566 (pmm) cc_final: 0.6166 (pmm) REVERT: B 83 GLU cc_start: 0.6888 (tp30) cc_final: 0.6498 (tp30) REVERT: I 70 LEU cc_start: 0.8360 (tt) cc_final: 0.8079 (tt) REVERT: I 73 MET cc_start: 0.6976 (tpt) cc_final: 0.5927 (tpt) REVERT: I 77 MET cc_start: 0.7583 (ptp) cc_final: 0.6660 (ptp) REVERT: I 107 ARG cc_start: 0.7403 (ttt-90) cc_final: 0.7118 (ttt-90) REVERT: I 108 HIS cc_start: 0.7285 (m170) cc_final: 0.7084 (m170) REVERT: I 146 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6474 (mtm) REVERT: A 18 MET cc_start: 0.7384 (mmm) cc_final: 0.7091 (tpp) REVERT: A 23 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.6862 (t70) REVERT: A 24 ILE cc_start: 0.7799 (mt) cc_final: 0.7387 (mt) REVERT: A 56 LYS cc_start: 0.8328 (mppt) cc_final: 0.8020 (mmtm) REVERT: A 57 LYS cc_start: 0.7379 (mtmt) cc_final: 0.7099 (mtmm) REVERT: A 61 ASP cc_start: 0.7108 (t70) cc_final: 0.6720 (t0) REVERT: A 88 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7714 (t) REVERT: A 132 ASP cc_start: 0.6400 (t70) cc_final: 0.6044 (t0) REVERT: A 171 SER cc_start: 0.8390 (t) cc_final: 0.7831 (p) REVERT: A 228 TYR cc_start: 0.8476 (m-80) cc_final: 0.8211 (m-80) REVERT: A 231 GLU cc_start: 0.6821 (tt0) cc_final: 0.6621 (tt0) REVERT: A 264 HIS cc_start: 0.7601 (m170) cc_final: 0.7294 (m170) REVERT: A 319 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.6950 (mtm-85) REVERT: A 387 ARG cc_start: 0.7745 (ptm160) cc_final: 0.7502 (ptm160) REVERT: A 603 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6717 (tpt) REVERT: A 701 MET cc_start: 0.7137 (mmt) cc_final: 0.6701 (mmt) REVERT: A 732 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7799 (ttp80) REVERT: A 765 GLU cc_start: 0.6789 (mp0) cc_final: 0.6342 (mp0) REVERT: A 768 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 872 LYS cc_start: 0.8646 (mttp) cc_final: 0.8164 (mttp) REVERT: A 956 MET cc_start: 0.7641 (tpp) cc_final: 0.7394 (tpp) REVERT: A 959 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: A 1084 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: A 1089 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7569 (mm) REVERT: A 1104 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7014 (mm-30) outliers start: 35 outliers final: 23 residues processed: 293 average time/residue: 0.1143 time to fit residues: 46.5703 Evaluate side-chains 299 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 139 optimal weight: 0.0270 chunk 129 optimal weight: 0.5980 chunk 95 optimal weight: 0.0010 chunk 22 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 overall best weight: 0.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 ASN ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 GLN A1264 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.163306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139898 restraints weight = 19349.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144630 restraints weight = 9195.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147717 restraints weight = 5442.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149751 restraints weight = 3720.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.150951 restraints weight = 2819.899| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12055 Z= 0.120 Angle : 0.653 9.741 16184 Z= 0.332 Chirality : 0.041 0.176 1726 Planarity : 0.004 0.050 2127 Dihedral : 6.820 131.797 1595 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.36 % Rotamer: Outliers : 1.94 % Allowed : 19.77 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.22), residues: 1441 helix: 1.54 (0.17), residues: 852 sheet: -1.47 (0.50), residues: 112 loop : -0.61 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 87 TYR 0.027 0.001 TYR A 718 PHE 0.034 0.002 PHE I 66 TRP 0.023 0.001 TRP A1253 HIS 0.003 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12055) covalent geometry : angle 0.65336 / 0.33 (16184) hydrogen bonds : bond 0.03639 / 2.36 ( 670) hydrogen bonds : angle 4.35753 / 3.14 ( 1965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.64 seconds wall clock time: 36 minutes 47.11 seconds (2207.11 seconds total)