Starting phenix.real_space_refine on Sat Jul 4 06:50:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe5_70387/07_2026/9oe5_70387_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe5_70387/07_2026/9oe5_70387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oe5_70387/07_2026/9oe5_70387_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe5_70387/07_2026/9oe5_70387_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oe5_70387/07_2026/9oe5_70387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe5_70387/07_2026/9oe5_70387.map" } resolution = 3.16 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5773 2.51 5 N 1534 2.21 5 O 1680 1.98 5 H 9161 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 18205 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 18141 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 27, 'TRANS': 1131} Chain breaks: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.98, per 1000 atoms: 0.16 Number of scatterers: 18205 At special positions: 0 Unit cell: (72.21, 119.52, 136.95, 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) S 49 16.00 P 6 15.00 Mg 2 11.99 O 1680 8.00 N 1534 7.00 C 5773 6.00 H 9161 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 657.6 milliseconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 69.1% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 49 through 83 removed outlier: 4.590A pdb=" N LEU A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 114 through 163 removed outlier: 4.174A pdb=" N HIS A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 172 through 180 removed outlier: 3.763A pdb=" N ASN A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.629A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 216 removed outlier: 3.897A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.510A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.037A pdb=" N GLY A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 252 Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 274 through 323 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.510A pdb=" N GLN A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 removed outlier: 4.682A pdb=" N ASN A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.602A pdb=" N THR A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 552 removed outlier: 4.044A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'A' and resid 593 through 598 removed outlier: 3.742A pdb=" N ILE A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.527A pdb=" N LYS A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.626A pdb=" N LEU A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 738 removed outlier: 3.818A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Proline residue: A 725 - end of helix removed outlier: 4.014A pdb=" N PHE A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 795 Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.845A pdb=" N ASP A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.633A pdb=" N VAL A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 827 Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 852 through 901 removed outlier: 3.598A pdb=" N THR A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Proline residue: A 864 - end of helix removed outlier: 4.144A pdb=" N GLN A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 894 " --> pdb=" O GLN A 890 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 912 through 964 removed outlier: 4.566A pdb=" N VAL A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Proline residue: A 925 - end of helix removed outlier: 3.748A pdb=" N SER A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 993 Processing helix chain 'A' and resid 995 through 1012 Processing helix chain 'A' and resid 1075 through 1080 removed outlier: 3.553A pdb=" N GLN A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.581A pdb=" N GLY A1132 " --> pdb=" O ILE A1129 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1129 through 1133' Processing helix chain 'A' and resid 1139 through 1150 Processing helix chain 'A' and resid 1152 through 1157 Processing helix chain 'A' and resid 1161 through 1165 removed outlier: 3.637A pdb=" N THR A1165 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1190 removed outlier: 4.358A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1220 Processing helix chain 'A' and resid 1231 through 1236 removed outlier: 3.656A pdb=" N GLN A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1261 removed outlier: 3.909A pdb=" N GLN A1261 " --> pdb=" O GLN A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1274 Processing sheet with id=AA1, first strand: chain 'A' and resid 402 through 404 removed outlier: 7.354A pdb=" N PHE A 404 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN A 416 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.387A pdb=" N LEU A 557 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 590 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 559 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 427 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ALA A 604 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA A 429 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N PHE A 606 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 431 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 613 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN A 607 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1051 through 1054 removed outlier: 3.517A pdb=" N GLY A1053 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL A1038 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1051 through 1054 removed outlier: 3.517A pdb=" N GLY A1053 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL A1038 " --> pdb=" O GLY A1053 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE A1035 " --> pdb=" O MET A1093 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N MET A1093 " --> pdb=" O PHE A1035 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS A1037 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG A1091 " --> pdb=" O HIS A1037 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1111 through 1114 removed outlier: 6.712A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A1228 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A1197 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A1064 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A1063 " --> pdb=" O CYS A1240 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA A1242 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA A1065 " --> pdb=" O ALA A1242 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A1244 " --> pdb=" O ALA A1065 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A1241 " --> pdb=" O GLN A1252 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN A1252 " --> pdb=" O ILE A1241 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A1243 " --> pdb=" O VAL A1250 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 9152 1.06 - 1.28: 1496 1.28 - 1.50: 3781 1.50 - 1.73: 3845 1.73 - 1.95: 87 Bond restraints: 18361 Sorted by residual: bond pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CA TYR A 802 " pdb=" C TYR A 802 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.37e-02 5.33e+03 1.67e+01 bond pdb=" O3A AGS A1304 " pdb=" PA AGS A1304 " ideal model delta sigma weight residual 1.664 1.585 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " ideal model delta sigma weight residual 1.664 1.589 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 18356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 32864 2.20 - 4.39: 308 4.39 - 6.59: 30 6.59 - 8.79: 11 8.79 - 10.98: 6 Bond angle restraints: 33219 Sorted by residual: angle pdb=" N ILE A1129 " pdb=" CA ILE A1129 " pdb=" C ILE A1129 " ideal model delta sigma weight residual 112.96 107.76 5.20 1.00e+00 1.00e+00 2.71e+01 angle pdb=" N GLN A1180 " pdb=" CA GLN A1180 " pdb=" CB GLN A1180 " ideal model delta sigma weight residual 111.06 119.16 -8.10 1.59e+00 3.96e-01 2.60e+01 angle pdb=" N GLN A1180 " pdb=" CA GLN A1180 " pdb=" C GLN A1180 " ideal model delta sigma weight residual 114.64 107.34 7.30 1.52e+00 4.33e-01 2.31e+01 angle pdb=" N ILE A1182 " pdb=" CA ILE A1182 " pdb=" C ILE A1182 " ideal model delta sigma weight residual 111.58 107.12 4.46 1.06e+00 8.90e-01 1.77e+01 angle pdb=" O3A AGS A1303 " pdb=" PB AGS A1303 " pdb=" O3B AGS A1303 " ideal model delta sigma weight residual 100.38 111.36 -10.98 3.00e+00 1.11e-01 1.34e+01 ... (remaining 33214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 8215 34.61 - 69.21: 358 69.21 - 103.82: 20 103.82 - 138.42: 6 138.42 - 173.03: 1 Dihedral angle restraints: 8600 sinusoidal: 4731 harmonic: 3869 Sorted by residual: dihedral pdb=" O2A AGS A1303 " pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sinusoidal sigma weight residual 307.72 134.69 173.03 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual 138.55 3.29 135.26 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" O3A AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual 252.61 124.68 127.93 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 8597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1225 0.055 - 0.110: 180 0.110 - 0.165: 29 0.165 - 0.220: 1 0.220 - 0.275: 2 Chirality restraints: 1437 Sorted by residual: chirality pdb=" C3' AGS A1303 " pdb=" C2' AGS A1303 " pdb=" C4' AGS A1303 " pdb=" O3' AGS A1303 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' AGS A1304 " pdb=" C2' AGS A1304 " pdb=" C4' AGS A1304 " pdb=" O3' AGS A1304 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CG LEU A1056 " pdb=" CB LEU A1056 " pdb=" CD1 LEU A1056 " pdb=" CD2 LEU A1056 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1434 not shown) Planarity restraints: 2701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1180 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLN A1180 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN A1180 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG A1181 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1180 " -0.019 2.00e-02 2.50e+03 2.15e-02 6.95e+00 pdb=" CD GLN A1180 " -0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN A1180 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN A1180 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A1180 " 0.032 2.00e-02 2.50e+03 pdb="HE22 GLN A1180 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 802 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" N ASP A 803 " -0.043 2.00e-02 2.50e+03 pdb=" CA ASP A 803 " 0.011 2.00e-02 2.50e+03 pdb=" H ASP A 803 " 0.019 2.00e-02 2.50e+03 ... (remaining 2698 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1438 2.22 - 2.81: 39211 2.81 - 3.41: 49368 3.41 - 4.00: 64288 4.00 - 4.60: 101051 Nonbonded interactions: 255356 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 438 " pdb="MG MG A1302 " model vdw 1.625 1.700 nonbonded pdb="HH11 ARG A 405 " pdb=" OE1 GLN A 452 " model vdw 1.656 2.450 nonbonded pdb=" O TRP A 801 " pdb="HD22 ASN A 807 " model vdw 1.666 2.450 nonbonded pdb=" OE2 GLU A 164 " pdb=" H ILE A 380 " model vdw 1.667 2.450 nonbonded pdb=" H LYS A 394 " pdb=" OD2 ASP A 459 " model vdw 1.673 2.450 ... (remaining 255351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.110 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 9200 Z= 0.204 Angle : 0.736 10.982 12444 Z= 0.378 Chirality : 0.041 0.275 1437 Planarity : 0.004 0.059 1572 Dihedral : 18.278 173.030 3415 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 1.67 % Allowed : 16.79 % Favored : 81.54 % 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: 1.04 (0.26), residues: 1153 helix: 1.58 (0.20), residues: 736 sheet: -0.82 (0.72), residues: 52 loop : -0.89 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 585 TYR 0.012 0.001 TYR A 802 PHE 0.012 0.001 PHE A 731 TRP 0.005 0.001 TRP A 853 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 ( 9200) covalent geometry : angle 0.73642 / 0.38 (12444) hydrogen bonds : bond 0.14217 / 9.38 ( 574) hydrogen bonds : angle 5.46908 / 4.00 ( 1692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8396 (t80) cc_final: 0.8078 (t80) REVERT: A 159 SER cc_start: 0.8860 (m) cc_final: 0.8542 (p) REVERT: A 321 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: A 536 MET cc_start: 0.8201 (mtp) cc_final: 0.7915 (mtp) REVERT: A 542 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 1246 ASN cc_start: 0.8280 (m-40) cc_final: 0.7950 (t0) outliers start: 16 outliers final: 14 residues processed: 79 average time/residue: 0.1412 time to fit residues: 17.3583 Evaluate side-chains 78 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.088667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068595 restraints weight = 66299.812| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.09 r_work: 0.3098 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9200 Z= 0.199 Angle : 0.519 6.135 12444 Z= 0.285 Chirality : 0.039 0.139 1437 Planarity : 0.004 0.048 1572 Dihedral : 12.636 143.057 1344 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 1.56 % Allowed : 17.00 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.08 (0.26), residues: 1153 helix: 1.68 (0.19), residues: 753 sheet: -0.88 (0.72), residues: 52 loop : -1.15 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1231 TYR 0.010 0.001 TYR A 123 PHE 0.009 0.001 PHE A 319 TRP 0.006 0.001 TRP A 853 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 9200) covalent geometry : angle 0.51892 / 0.29 (12444) hydrogen bonds : bond 0.04734 / 3.14 ( 574) hydrogen bonds : angle 4.36904 / 3.13 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8406 (t80) cc_final: 0.8129 (t80) REVERT: A 321 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: A 542 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 1094 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9215 (mp) REVERT: A 1246 ASN cc_start: 0.8429 (m-40) cc_final: 0.8056 (t0) outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.1495 time to fit residues: 17.6242 Evaluate side-chains 75 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 928 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.089317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.069511 restraints weight = 66551.831| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.04 r_work: 0.3127 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9200 Z= 0.146 Angle : 0.475 5.263 12444 Z= 0.257 Chirality : 0.037 0.139 1437 Planarity : 0.003 0.040 1572 Dihedral : 9.851 136.124 1332 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 2.09 % Allowed : 15.85 % Favored : 82.06 % 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: 1.32 (0.26), residues: 1153 helix: 1.90 (0.19), residues: 752 sheet: -0.81 (0.72), residues: 52 loop : -1.16 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.008 0.001 TYR A 981 PHE 0.009 0.001 PHE A 731 TRP 0.004 0.001 TRP A 853 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 9200) covalent geometry : angle 0.47475 / 0.26 (12444) hydrogen bonds : bond 0.04446 / 2.94 ( 574) hydrogen bonds : angle 4.13052 / 2.96 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8417 (t80) cc_final: 0.8117 (t80) REVERT: A 321 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: A 542 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 560 ASP cc_start: 0.7891 (t0) cc_final: 0.7304 (t0) REVERT: A 1094 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9193 (mp) outliers start: 20 outliers final: 14 residues processed: 81 average time/residue: 0.1508 time to fit residues: 19.1370 Evaluate side-chains 77 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.089692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.069492 restraints weight = 66263.436| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.12 r_work: 0.3113 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9200 Z= 0.135 Angle : 0.460 5.328 12444 Z= 0.250 Chirality : 0.037 0.136 1437 Planarity : 0.003 0.036 1572 Dihedral : 9.029 136.341 1330 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 1.77 % Allowed : 16.27 % Favored : 81.96 % 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: 1.43 (0.26), residues: 1153 helix: 2.02 (0.19), residues: 753 sheet: -0.68 (0.73), residues: 51 loop : -1.23 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.008 0.001 TYR A 981 PHE 0.008 0.001 PHE A 731 TRP 0.004 0.001 TRP A 853 HIS 0.002 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9200) covalent geometry : angle 0.45964 / 0.25 (12444) hydrogen bonds : bond 0.04160 / 2.76 ( 574) hydrogen bonds : angle 4.00857 / 2.88 ( 1692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8404 (t80) cc_final: 0.8105 (t80) REVERT: A 304 MET cc_start: 0.8478 (tpp) cc_final: 0.8208 (tpt) REVERT: A 321 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: A 560 ASP cc_start: 0.7866 (t0) cc_final: 0.7242 (t0) REVERT: A 900 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8777 (mm-30) REVERT: A 1094 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9183 (mp) outliers start: 17 outliers final: 13 residues processed: 77 average time/residue: 0.1484 time to fit residues: 17.9795 Evaluate side-chains 76 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.089619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.069891 restraints weight = 66014.311| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.01 r_work: 0.3114 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9200 Z= 0.136 Angle : 0.445 5.364 12444 Z= 0.242 Chirality : 0.037 0.140 1437 Planarity : 0.003 0.036 1572 Dihedral : 8.361 137.354 1328 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 1.88 % Allowed : 16.16 % Favored : 81.96 % 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: 1.53 (0.26), residues: 1153 helix: 2.12 (0.19), residues: 752 sheet: -0.78 (0.72), residues: 52 loop : -1.21 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.008 0.001 TYR A 981 PHE 0.008 0.001 PHE A 731 TRP 0.004 0.001 TRP A 141 HIS 0.002 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 9200) covalent geometry : angle 0.44541 / 0.24 (12444) hydrogen bonds : bond 0.04078 / 2.68 ( 574) hydrogen bonds : angle 3.92825 / 2.82 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8398 (t80) cc_final: 0.8105 (t80) REVERT: A 304 MET cc_start: 0.8481 (tpp) cc_final: 0.8207 (tpt) REVERT: A 321 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: A 542 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 560 ASP cc_start: 0.7914 (t0) cc_final: 0.7289 (t0) REVERT: A 1094 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9152 (mp) outliers start: 18 outliers final: 16 residues processed: 78 average time/residue: 0.1554 time to fit residues: 19.0494 Evaluate side-chains 77 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 17 optimal weight: 0.0270 chunk 75 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.090628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.070946 restraints weight = 65990.420| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.01 r_work: 0.3148 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9200 Z= 0.106 Angle : 0.440 6.853 12444 Z= 0.235 Chirality : 0.037 0.138 1437 Planarity : 0.003 0.036 1572 Dihedral : 8.172 137.408 1328 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.10 % Rotamer: Outliers : 1.67 % Allowed : 16.58 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.68 (0.26), residues: 1153 helix: 2.24 (0.19), residues: 756 sheet: -0.66 (0.73), residues: 51 loop : -1.22 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 582 TYR 0.008 0.001 TYR A 981 PHE 0.007 0.001 PHE A 731 TRP 0.004 0.001 TRP A 217 HIS 0.001 0.000 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 9200) covalent geometry : angle 0.44009 / 0.24 (12444) hydrogen bonds : bond 0.03924 / 2.59 ( 574) hydrogen bonds : angle 3.79891 / 2.74 ( 1692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8361 (t80) cc_final: 0.8071 (t80) REVERT: A 304 MET cc_start: 0.8492 (tpp) cc_final: 0.8225 (tpt) REVERT: A 321 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: A 560 ASP cc_start: 0.7936 (t0) cc_final: 0.7288 (t0) REVERT: A 1094 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9131 (mp) outliers start: 16 outliers final: 13 residues processed: 74 average time/residue: 0.1614 time to fit residues: 18.7270 Evaluate side-chains 74 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 32 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.090181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.070476 restraints weight = 66630.898| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.01 r_work: 0.3145 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9200 Z= 0.128 Angle : 0.438 5.374 12444 Z= 0.237 Chirality : 0.037 0.138 1437 Planarity : 0.003 0.036 1572 Dihedral : 8.099 138.472 1328 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 2.09 % Allowed : 16.37 % Favored : 81.54 % 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: 1.73 (0.26), residues: 1153 helix: 2.28 (0.19), residues: 756 sheet: -0.72 (0.73), residues: 52 loop : -1.19 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 543 TYR 0.008 0.001 TYR A 981 PHE 0.007 0.001 PHE A 319 TRP 0.003 0.001 TRP A 141 HIS 0.002 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 9200) covalent geometry : angle 0.43808 / 0.24 (12444) hydrogen bonds : bond 0.03909 / 2.57 ( 574) hydrogen bonds : angle 3.80705 / 2.74 ( 1692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8368 (t80) cc_final: 0.8076 (t80) REVERT: A 321 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: A 542 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8018 (tm-30) REVERT: A 560 ASP cc_start: 0.7945 (t0) cc_final: 0.7308 (t0) REVERT: A 1094 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9117 (mp) outliers start: 20 outliers final: 17 residues processed: 77 average time/residue: 0.1460 time to fit residues: 17.5932 Evaluate side-chains 79 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.089601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.070068 restraints weight = 66407.311| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.92 r_work: 0.3134 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9200 Z= 0.156 Angle : 0.451 5.465 12444 Z= 0.246 Chirality : 0.037 0.136 1437 Planarity : 0.003 0.036 1572 Dihedral : 8.046 140.766 1328 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 2.09 % Allowed : 16.06 % Favored : 81.86 % 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: 1.71 (0.26), residues: 1153 helix: 2.26 (0.19), residues: 756 sheet: -0.72 (0.73), residues: 52 loop : -1.17 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1057 TYR 0.008 0.001 TYR A 981 PHE 0.008 0.001 PHE A 272 TRP 0.004 0.001 TRP A 141 HIS 0.003 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 9200) covalent geometry : angle 0.45147 / 0.25 (12444) hydrogen bonds : bond 0.03988 / 2.62 ( 574) hydrogen bonds : angle 3.85274 / 2.77 ( 1692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8385 (t80) cc_final: 0.8093 (t80) REVERT: A 321 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: A 542 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 560 ASP cc_start: 0.7963 (t0) cc_final: 0.7329 (t0) REVERT: A 1094 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9123 (mp) outliers start: 20 outliers final: 18 residues processed: 76 average time/residue: 0.1444 time to fit residues: 17.1992 Evaluate side-chains 79 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.089129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.069406 restraints weight = 66487.459| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.99 r_work: 0.3112 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9200 Z= 0.168 Angle : 0.459 5.491 12444 Z= 0.250 Chirality : 0.037 0.136 1437 Planarity : 0.003 0.038 1572 Dihedral : 8.001 142.596 1328 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 2.09 % Allowed : 15.95 % Favored : 81.96 % 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: 1.70 (0.26), residues: 1153 helix: 2.24 (0.19), residues: 756 sheet: -0.74 (0.72), residues: 52 loop : -1.15 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 543 TYR 0.008 0.001 TYR A 981 PHE 0.008 0.001 PHE A 272 TRP 0.004 0.001 TRP A 141 HIS 0.003 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 9200) covalent geometry : angle 0.45880 / 0.25 (12444) hydrogen bonds : bond 0.04027 / 2.64 ( 574) hydrogen bonds : angle 3.89501 / 2.79 ( 1692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8397 (t80) cc_final: 0.8099 (t80) REVERT: A 321 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 542 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 560 ASP cc_start: 0.7947 (t0) cc_final: 0.7299 (t0) REVERT: A 1094 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9117 (mp) outliers start: 20 outliers final: 18 residues processed: 77 average time/residue: 0.1523 time to fit residues: 17.9243 Evaluate side-chains 79 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.090677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071155 restraints weight = 66203.198| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.92 r_work: 0.3153 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9200 Z= 0.115 Angle : 0.443 5.395 12444 Z= 0.236 Chirality : 0.037 0.138 1437 Planarity : 0.003 0.036 1572 Dihedral : 7.939 142.366 1328 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.98 % Allowed : 16.06 % Favored : 81.96 % 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: 1.85 (0.26), residues: 1153 helix: 2.36 (0.19), residues: 756 sheet: -0.70 (0.73), residues: 52 loop : -1.11 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 364 TYR 0.008 0.001 TYR A 981 PHE 0.006 0.001 PHE A 485 TRP 0.004 0.001 TRP A 217 HIS 0.001 0.000 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9200) covalent geometry : angle 0.44254 / 0.24 (12444) hydrogen bonds : bond 0.03869 / 2.53 ( 574) hydrogen bonds : angle 3.75876 / 2.70 ( 1692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1075 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8396 (t80) cc_final: 0.8106 (t80) REVERT: A 321 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: A 542 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 560 ASP cc_start: 0.7961 (t0) cc_final: 0.7330 (t0) REVERT: A 1094 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9107 (mp) outliers start: 19 outliers final: 17 residues processed: 76 average time/residue: 0.1415 time to fit residues: 16.9449 Evaluate side-chains 78 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.090591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071003 restraints weight = 66296.392| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.99 r_work: 0.3148 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9200 Z= 0.120 Angle : 0.443 5.407 12444 Z= 0.237 Chirality : 0.037 0.139 1437 Planarity : 0.003 0.036 1572 Dihedral : 7.850 142.180 1328 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.98 % Allowed : 16.27 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.88 (0.26), residues: 1153 helix: 2.38 (0.19), residues: 758 sheet: -0.69 (0.73), residues: 52 loop : -1.11 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 543 TYR 0.008 0.001 TYR A 981 PHE 0.007 0.001 PHE A 319 TRP 0.004 0.001 TRP A 141 HIS 0.002 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9200) covalent geometry : angle 0.44263 / 0.24 (12444) hydrogen bonds : bond 0.03831 / 2.51 ( 574) hydrogen bonds : angle 3.75389 / 2.70 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3459.14 seconds wall clock time: 59 minutes 24.13 seconds (3564.13 seconds total)