Starting phenix.real_space_refine on Sun Jun 8 18:22:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bwq_16294/06_2025/8bwq_16294.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bwq_16294/06_2025/8bwq_16294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bwq_16294/06_2025/8bwq_16294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bwq_16294/06_2025/8bwq_16294.map" model { file = "/net/cci-nas-00/data/ceres_data/8bwq_16294/06_2025/8bwq_16294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bwq_16294/06_2025/8bwq_16294.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6224 2.51 5 N 1605 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9576 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'TTC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.70, per 1000 atoms: 0.70 Number of scatterers: 9576 At special positions: 0 Unit cell: (77.376, 108.16, 146.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1704 8.00 N 1605 7.00 C 6224 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: 2.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 73.6% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.808A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 4.301A pdb=" N LYS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 122 removed outlier: 4.916A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 4.111A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 Processing helix chain 'A' and resid 150 through 181 removed outlier: 4.027A pdb=" N LEU A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.608A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 removed outlier: 4.475A pdb=" N GLN A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 235 through 290 removed outlier: 3.897A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.723A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 342 removed outlier: 3.797A pdb=" N LEU A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.868A pdb=" N ALA A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.522A pdb=" N GLU A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 512 through 522 removed outlier: 4.163A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.631A pdb=" N ARG A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 removed outlier: 4.688A pdb=" N PHE A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 582 through 585 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 697 through 707 removed outlier: 4.080A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.532A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 removed outlier: 3.929A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.851A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.957A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'A' and resid 835 through 861 Processing helix chain 'A' and resid 864 through 910 removed outlier: 4.163A pdb=" N VAL A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) Proline residue: A 870 - end of helix removed outlier: 4.078A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.016A pdb=" N GLU A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1007 removed outlier: 3.660A pdb=" N THR A 988 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1018 removed outlier: 3.880A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 3.972A pdb=" N GLU A1157 " --> pdb=" O GLN A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1279 through 1291 removed outlier: 3.785A pdb=" N ALA A1283 " --> pdb=" O ALA A1279 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1291 " --> pdb=" O THR A1287 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 6.684A pdb=" N GLN A 429 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR A 416 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 431 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.976A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 5.848A pdb=" N LYS A1059 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A1048 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA A1063 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASP A1044 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A1065 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE A1042 " --> pdb=" O ILE A1065 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1197 through 1201 removed outlier: 6.162A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1729 1.32 - 1.45: 2420 1.45 - 1.57: 5563 1.57 - 1.69: 2 1.69 - 1.81: 70 Bond restraints: 9784 Sorted by residual: bond pdb=" C14 TTC A1401 " pdb=" N12 TTC A1401 " ideal model delta sigma weight residual 1.375 1.479 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C11 TTC A1401 " pdb=" N12 TTC A1401 " ideal model delta sigma weight residual 1.463 1.533 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C13 TTC A1401 " pdb=" C9 TTC A1401 " ideal model delta sigma weight residual 1.456 1.523 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C14 TTC A1401 " pdb=" C15 TTC A1401 " ideal model delta sigma weight residual 1.441 1.508 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C20 TTC A1401 " pdb=" O22 TTC A1401 " ideal model delta sigma weight residual 1.320 1.381 -0.061 2.00e-02 2.50e+03 9.20e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 12425 1.63 - 3.27: 701 3.27 - 4.90: 99 4.90 - 6.54: 33 6.54 - 8.17: 10 Bond angle restraints: 13268 Sorted by residual: angle pdb=" CA TYR A 985 " pdb=" CB TYR A 985 " pdb=" CG TYR A 985 " ideal model delta sigma weight residual 113.90 108.55 5.35 1.80e+00 3.09e-01 8.82e+00 angle pdb=" C LEU A 341 " pdb=" N LEU A 342 " pdb=" CA LEU A 342 " ideal model delta sigma weight residual 122.31 116.79 5.52 2.00e+00 2.50e-01 7.62e+00 angle pdb=" N PHE A 205 " pdb=" CA PHE A 205 " pdb=" C PHE A 205 " ideal model delta sigma weight residual 112.38 115.65 -3.27 1.22e+00 6.72e-01 7.20e+00 angle pdb=" C CYS A 161 " pdb=" N ALA A 162 " pdb=" CA ALA A 162 " ideal model delta sigma weight residual 120.28 116.84 3.44 1.34e+00 5.57e-01 6.58e+00 angle pdb=" C LEU A 730 " pdb=" N GLN A 731 " pdb=" CA GLN A 731 " ideal model delta sigma weight residual 120.44 117.20 3.24 1.30e+00 5.92e-01 6.22e+00 ... (remaining 13263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5419 17.60 - 35.21: 340 35.21 - 52.81: 61 52.81 - 70.41: 10 70.41 - 88.02: 13 Dihedral angle restraints: 5843 sinusoidal: 2349 harmonic: 3494 Sorted by residual: dihedral pdb=" CA ASP A 834 " pdb=" C ASP A 834 " pdb=" N LEU A 835 " pdb=" CA LEU A 835 " ideal model delta harmonic sigma weight residual 180.00 -150.62 -29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ARG A 37 " pdb=" C ARG A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLN A1154 " pdb=" C GLN A1154 " pdb=" N LEU A1155 " pdb=" CA LEU A1155 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 915 0.041 - 0.081: 441 0.081 - 0.122: 138 0.122 - 0.163: 42 0.163 - 0.204: 2 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA HIS A 158 " pdb=" N HIS A 158 " pdb=" C HIS A 158 " pdb=" CB HIS A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE A 205 " pdb=" N PHE A 205 " pdb=" C PHE A 205 " pdb=" CB PHE A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA LYS A1102 " pdb=" N LYS A1102 " pdb=" C LYS A1102 " pdb=" CB LYS A1102 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 1535 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 TTC A1401 " -0.016 2.00e-02 2.50e+03 2.61e-02 3.75e+01 pdb=" C11 TTC A1401 " 0.036 2.00e-02 2.50e+03 pdb=" C13 TTC A1401 " 0.041 2.00e-02 2.50e+03 pdb=" C14 TTC A1401 " -0.019 2.00e-02 2.50e+03 pdb=" C15 TTC A1401 " -0.018 2.00e-02 2.50e+03 pdb=" C16 TTC A1401 " -0.002 2.00e-02 2.50e+03 pdb=" C17 TTC A1401 " 0.029 2.00e-02 2.50e+03 pdb=" C19 TTC A1401 " -0.054 2.00e-02 2.50e+03 pdb=" C2 TTC A1401 " -0.019 2.00e-02 2.50e+03 pdb=" C21 TTC A1401 " -0.010 2.00e-02 2.50e+03 pdb=" C27 TTC A1401 " -0.009 2.00e-02 2.50e+03 pdb=" C3 TTC A1401 " -0.018 2.00e-02 2.50e+03 pdb=" C4 TTC A1401 " -0.005 2.00e-02 2.50e+03 pdb=" C5 TTC A1401 " 0.004 2.00e-02 2.50e+03 pdb=" C6 TTC A1401 " 0.005 2.00e-02 2.50e+03 pdb=" C7 TTC A1401 " 0.016 2.00e-02 2.50e+03 pdb=" C8 TTC A1401 " 0.030 2.00e-02 2.50e+03 pdb=" C9 TTC A1401 " 0.046 2.00e-02 2.50e+03 pdb=" N10 TTC A1401 " 0.018 2.00e-02 2.50e+03 pdb=" N12 TTC A1401 " 0.014 2.00e-02 2.50e+03 pdb=" O18 TTC A1401 " -0.035 2.00e-02 2.50e+03 pdb=" O26 TTC A1401 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 917 " 0.002 2.00e-02 2.50e+03 1.90e-02 7.25e+00 pdb=" CG TYR A 917 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 917 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 917 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 917 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 917 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 917 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 917 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.003 2.00e-02 2.50e+03 1.80e-02 6.46e+00 pdb=" CG TYR A 157 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " 0.026 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1914 2.77 - 3.30: 10627 3.30 - 3.84: 15887 3.84 - 4.37: 19330 4.37 - 4.90: 31439 Nonbonded interactions: 79197 Sorted by model distance: nonbonded pdb=" O GLU A 521 " pdb=" OG1 THR A 526 " model vdw 2.238 3.040 nonbonded pdb=" ND1 HIS A 35 " pdb=" OE1 GLU A 884 " model vdw 2.246 3.120 nonbonded pdb=" O GLN A1068 " pdb=" NZ LYS A1070 " model vdw 2.265 3.120 nonbonded pdb=" O SER A 563 " pdb=" NE2 GLN A 593 " model vdw 2.362 3.120 nonbonded pdb=" NH1 ARG A1220 " pdb=" OD2 ASP A1240 " model vdw 2.365 3.120 ... (remaining 79192 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=0.00 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 9784 Z= 0.406 Angle : 0.890 8.171 13268 Z= 0.478 Chirality : 0.052 0.204 1538 Planarity : 0.008 0.087 1642 Dihedral : 13.092 88.017 3577 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1187 helix: -1.06 (0.16), residues: 770 sheet: -0.45 (0.50), residues: 72 loop : 0.16 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 89 HIS 0.007 0.002 HIS A 798 PHE 0.026 0.003 PHE A 418 TYR 0.030 0.006 TYR A 917 ARG 0.020 0.002 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.21707 ( 634) hydrogen bonds : angle 8.41699 ( 1815) covalent geometry : bond 0.00918 ( 9784) covalent geometry : angle 0.88977 (13268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.169 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: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8134 (mt) cc_final: 0.7857 (tt) REVERT: A 63 PHE cc_start: 0.8844 (m-80) cc_final: 0.8610 (m-10) REVERT: A 142 THR cc_start: 0.9443 (m) cc_final: 0.9205 (p) REVERT: A 241 MET cc_start: 0.8749 (mmm) cc_final: 0.8411 (mpp) REVERT: A 333 PHE cc_start: 0.8903 (t80) cc_final: 0.8355 (t80) REVERT: A 337 THR cc_start: 0.9118 (m) cc_final: 0.8832 (m) REVERT: A 388 THR cc_start: 0.9039 (m) cc_final: 0.8625 (m) REVERT: A 415 PHE cc_start: 0.8862 (t80) cc_final: 0.8562 (t80) REVERT: A 558 LEU cc_start: 0.8099 (mt) cc_final: 0.7780 (tt) REVERT: A 577 CYS cc_start: 0.7907 (t) cc_final: 0.7463 (t) REVERT: A 1025 TRP cc_start: 0.8416 (m-10) cc_final: 0.7852 (m-10) REVERT: A 1043 PHE cc_start: 0.8570 (m-80) cc_final: 0.8199 (m-80) REVERT: A 1048 PHE cc_start: 0.7964 (t80) cc_final: 0.7509 (t80) REVERT: A 1069 GLU cc_start: 0.7876 (tt0) cc_final: 0.7650 (tp30) REVERT: A 1112 ASP cc_start: 0.7089 (m-30) cc_final: 0.6567 (m-30) REVERT: A 1120 ILE cc_start: 0.9253 (mt) cc_final: 0.8989 (mm) REVERT: A 1131 MET cc_start: 0.8803 (mmm) cc_final: 0.8588 (mmm) REVERT: A 1191 ILE cc_start: 0.9088 (mt) cc_final: 0.8851 (mt) REVERT: A 1201 ASP cc_start: 0.7276 (t0) cc_final: 0.7055 (t70) REVERT: A 1230 THR cc_start: 0.9250 (m) cc_final: 0.8920 (p) REVERT: A 1241 SER cc_start: 0.8639 (m) cc_final: 0.8382 (p) REVERT: A 1251 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7563 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2636 time to fit residues: 85.6834 Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 183 ASN A 399 ASN A 602 GLN A 703 ASN A 903 HIS A1263 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092725 restraints weight = 22035.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095956 restraints weight = 11349.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098012 restraints weight = 7331.347| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9784 Z= 0.213 Angle : 0.701 6.831 13268 Z= 0.373 Chirality : 0.044 0.163 1538 Planarity : 0.005 0.066 1642 Dihedral : 8.331 71.852 1308 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.11 % Allowed : 8.45 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1187 helix: 0.44 (0.17), residues: 793 sheet: -0.16 (0.55), residues: 68 loop : 0.41 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 89 HIS 0.008 0.001 HIS A1141 PHE 0.031 0.002 PHE A 258 TYR 0.025 0.002 TYR A 499 ARG 0.014 0.001 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.05720 ( 634) hydrogen bonds : angle 5.20017 ( 1815) covalent geometry : bond 0.00467 ( 9784) covalent geometry : angle 0.70077 (13268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 1.358 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8192 (mt) cc_final: 0.7945 (tt) REVERT: A 241 MET cc_start: 0.8918 (mmm) cc_final: 0.8663 (tpp) REVERT: A 289 TYR cc_start: 0.8093 (m-10) cc_final: 0.7868 (m-80) REVERT: A 415 PHE cc_start: 0.8850 (t80) cc_final: 0.8606 (t80) REVERT: A 418 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: A 490 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8049 (mmm160) REVERT: A 550 TYR cc_start: 0.7844 (t80) cc_final: 0.7143 (t80) REVERT: A 558 LEU cc_start: 0.8290 (mt) cc_final: 0.7701 (tt) REVERT: A 589 LEU cc_start: 0.8587 (tp) cc_final: 0.8306 (tp) REVERT: A 990 MET cc_start: 0.8204 (tpp) cc_final: 0.7908 (tpp) REVERT: A 1069 GLU cc_start: 0.8057 (tt0) cc_final: 0.7650 (tp30) REVERT: A 1120 ILE cc_start: 0.9364 (mt) cc_final: 0.9145 (mm) REVERT: A 1128 THR cc_start: 0.7736 (m) cc_final: 0.7319 (m) REVERT: A 1201 ASP cc_start: 0.7145 (t0) cc_final: 0.6882 (t70) REVERT: A 1235 LEU cc_start: 0.9196 (mp) cc_final: 0.8840 (tt) outliers start: 22 outliers final: 15 residues processed: 204 average time/residue: 0.2695 time to fit residues: 79.3423 Evaluate side-chains 181 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 40.0000 chunk 102 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.131904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095392 restraints weight = 22389.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.098760 restraints weight = 11292.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100857 restraints weight = 7188.562| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.135 Angle : 0.600 7.859 13268 Z= 0.314 Chirality : 0.041 0.172 1538 Planarity : 0.004 0.050 1642 Dihedral : 7.152 69.164 1308 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.40 % Allowed : 11.71 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1187 helix: 0.94 (0.18), residues: 785 sheet: 0.21 (0.58), residues: 68 loop : 0.57 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 89 HIS 0.007 0.001 HIS A1111 PHE 0.029 0.002 PHE A 258 TYR 0.022 0.001 TYR A1016 ARG 0.004 0.000 ARG A1220 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 634) hydrogen bonds : angle 4.70722 ( 1815) covalent geometry : bond 0.00275 ( 9784) covalent geometry : angle 0.60015 (13268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8133 (mt) cc_final: 0.7916 (tt) REVERT: A 103 GLU cc_start: 0.7553 (pp20) cc_final: 0.7351 (pp20) REVERT: A 289 TYR cc_start: 0.8020 (m-10) cc_final: 0.7448 (m-80) REVERT: A 418 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: A 495 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: A 550 TYR cc_start: 0.8021 (t80) cc_final: 0.7320 (t80) REVERT: A 558 LEU cc_start: 0.8243 (mt) cc_final: 0.7682 (tt) REVERT: A 589 LEU cc_start: 0.8539 (tp) cc_final: 0.8308 (tp) REVERT: A 605 ILE cc_start: 0.6769 (mm) cc_final: 0.6434 (mm) REVERT: A 990 MET cc_start: 0.8294 (tpp) cc_final: 0.8016 (tpp) REVERT: A 1043 PHE cc_start: 0.8287 (m-80) cc_final: 0.7881 (m-80) REVERT: A 1111 HIS cc_start: 0.7235 (m170) cc_final: 0.6782 (m170) REVERT: A 1120 ILE cc_start: 0.9394 (mt) cc_final: 0.9174 (mm) REVERT: A 1151 GLN cc_start: 0.9038 (tt0) cc_final: 0.8802 (pt0) REVERT: A 1201 ASP cc_start: 0.7539 (t0) cc_final: 0.7238 (t70) REVERT: A 1216 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8856 (tp-100) REVERT: A 1270 TYR cc_start: 0.8177 (t80) cc_final: 0.7872 (t80) outliers start: 25 outliers final: 16 residues processed: 213 average time/residue: 0.2233 time to fit residues: 68.1011 Evaluate side-chains 178 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1211 THR Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1244 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.130499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094229 restraints weight = 22065.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097436 restraints weight = 11270.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.099530 restraints weight = 7205.879| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9784 Z= 0.153 Angle : 0.617 11.149 13268 Z= 0.316 Chirality : 0.040 0.143 1538 Planarity : 0.004 0.031 1642 Dihedral : 6.573 64.802 1308 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 14.30 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1187 helix: 1.08 (0.18), residues: 787 sheet: 0.37 (0.55), residues: 79 loop : 0.58 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 89 HIS 0.008 0.001 HIS A1141 PHE 0.027 0.002 PHE A 258 TYR 0.017 0.001 TYR A1259 ARG 0.004 0.000 ARG A1182 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 634) hydrogen bonds : angle 4.63423 ( 1815) covalent geometry : bond 0.00337 ( 9784) covalent geometry : angle 0.61675 (13268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7509 (pp20) cc_final: 0.7262 (pp20) REVERT: A 221 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: A 418 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: A 493 ILE cc_start: 0.9188 (mm) cc_final: 0.8499 (tp) REVERT: A 495 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: A 550 TYR cc_start: 0.8067 (t80) cc_final: 0.7280 (t80) REVERT: A 558 LEU cc_start: 0.8197 (mt) cc_final: 0.7753 (tt) REVERT: A 605 ILE cc_start: 0.6783 (mm) cc_final: 0.6554 (mm) REVERT: A 887 ARG cc_start: 0.7986 (ptt90) cc_final: 0.7770 (ptt90) REVERT: A 1069 GLU cc_start: 0.8199 (tp30) cc_final: 0.7941 (tp30) REVERT: A 1090 ARG cc_start: 0.8535 (mtp180) cc_final: 0.7965 (tpt-90) REVERT: A 1120 ILE cc_start: 0.9415 (mt) cc_final: 0.9184 (mm) REVERT: A 1182 ARG cc_start: 0.8553 (mtp180) cc_final: 0.8239 (mtm180) REVERT: A 1201 ASP cc_start: 0.7721 (t0) cc_final: 0.7268 (t70) REVERT: A 1216 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8882 (tp-100) REVERT: A 1280 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8568 (mp0) outliers start: 32 outliers final: 20 residues processed: 196 average time/residue: 0.1991 time to fit residues: 57.0247 Evaluate side-chains 177 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1211 THR Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1280 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093221 restraints weight = 22066.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096401 restraints weight = 11333.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098472 restraints weight = 7330.106| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9784 Z= 0.146 Angle : 0.620 9.419 13268 Z= 0.312 Chirality : 0.040 0.147 1538 Planarity : 0.004 0.031 1642 Dihedral : 6.146 57.164 1308 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.84 % Allowed : 15.45 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1187 helix: 1.26 (0.18), residues: 786 sheet: 0.62 (0.54), residues: 79 loop : 0.62 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1025 HIS 0.007 0.001 HIS A1141 PHE 0.026 0.001 PHE A 258 TYR 0.023 0.002 TYR A1259 ARG 0.004 0.000 ARG A1251 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 634) hydrogen bonds : angle 4.54866 ( 1815) covalent geometry : bond 0.00320 ( 9784) covalent geometry : angle 0.62026 (13268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.7732 (mmp) cc_final: 0.6449 (tmm) REVERT: A 221 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: A 236 SER cc_start: 0.8590 (m) cc_final: 0.8352 (m) REVERT: A 409 MET cc_start: 0.4307 (pmm) cc_final: 0.3151 (mmt) REVERT: A 418 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: A 493 ILE cc_start: 0.9185 (mm) cc_final: 0.8515 (tp) REVERT: A 495 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: A 550 TYR cc_start: 0.8136 (t80) cc_final: 0.7347 (t80) REVERT: A 558 LEU cc_start: 0.8249 (mt) cc_final: 0.7716 (tt) REVERT: A 1069 GLU cc_start: 0.8238 (tp30) cc_final: 0.7996 (tp30) REVERT: A 1090 ARG cc_start: 0.8526 (mtp180) cc_final: 0.7880 (tpt-90) REVERT: A 1114 ARG cc_start: 0.9003 (mtt180) cc_final: 0.8542 (mtt-85) REVERT: A 1120 ILE cc_start: 0.9422 (mt) cc_final: 0.9184 (mm) REVERT: A 1201 ASP cc_start: 0.7661 (t0) cc_final: 0.7187 (t70) REVERT: A 1280 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8672 (mp0) outliers start: 40 outliers final: 24 residues processed: 196 average time/residue: 0.1929 time to fit residues: 54.8783 Evaluate side-chains 178 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1280 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 71 optimal weight: 0.0170 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095500 restraints weight = 22045.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098440 restraints weight = 11593.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100356 restraints weight = 7634.379| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9784 Z= 0.126 Angle : 0.603 8.266 13268 Z= 0.304 Chirality : 0.040 0.151 1538 Planarity : 0.004 0.036 1642 Dihedral : 5.880 48.992 1308 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.59 % Allowed : 17.27 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1187 helix: 1.38 (0.18), residues: 785 sheet: 0.79 (0.56), residues: 79 loop : 0.69 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 863 HIS 0.007 0.001 HIS A1111 PHE 0.024 0.001 PHE A 258 TYR 0.020 0.001 TYR A1259 ARG 0.003 0.000 ARG A1251 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 634) hydrogen bonds : angle 4.43586 ( 1815) covalent geometry : bond 0.00267 ( 9784) covalent geometry : angle 0.60278 (13268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7500 (pp20) cc_final: 0.7200 (pp20) REVERT: A 221 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: A 236 SER cc_start: 0.8517 (m) cc_final: 0.8294 (m) REVERT: A 418 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: A 493 ILE cc_start: 0.9198 (mm) cc_final: 0.8591 (tp) REVERT: A 495 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: A 550 TYR cc_start: 0.8140 (t80) cc_final: 0.7366 (t80) REVERT: A 558 LEU cc_start: 0.8242 (mt) cc_final: 0.7773 (tt) REVERT: A 874 ILE cc_start: 0.8961 (mt) cc_final: 0.8721 (mm) REVERT: A 887 ARG cc_start: 0.7862 (ptt90) cc_final: 0.7459 (ptt90) REVERT: A 990 MET cc_start: 0.8012 (tpp) cc_final: 0.7782 (tpp) REVERT: A 1061 LEU cc_start: 0.8720 (tt) cc_final: 0.8361 (mm) REVERT: A 1069 GLU cc_start: 0.8225 (tp30) cc_final: 0.7970 (tp30) REVERT: A 1120 ILE cc_start: 0.9415 (mt) cc_final: 0.9190 (mm) REVERT: A 1201 ASP cc_start: 0.7620 (t0) cc_final: 0.7227 (t70) REVERT: A 1235 LEU cc_start: 0.9198 (mt) cc_final: 0.8363 (tt) outliers start: 27 outliers final: 20 residues processed: 189 average time/residue: 0.2141 time to fit residues: 59.1417 Evaluate side-chains 177 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1244 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 0.0010 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 HIS A1274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.130790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094746 restraints weight = 22079.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097696 restraints weight = 11649.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099669 restraints weight = 7669.086| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9784 Z= 0.135 Angle : 0.620 9.847 13268 Z= 0.311 Chirality : 0.041 0.169 1538 Planarity : 0.004 0.039 1642 Dihedral : 5.741 49.579 1308 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.98 % Allowed : 18.33 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1187 helix: 1.45 (0.18), residues: 781 sheet: 0.76 (0.55), residues: 79 loop : 0.66 (0.38), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 863 HIS 0.006 0.001 HIS A1141 PHE 0.023 0.001 PHE A 258 TYR 0.018 0.001 TYR A1259 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 634) hydrogen bonds : angle 4.42150 ( 1815) covalent geometry : bond 0.00297 ( 9784) covalent geometry : angle 0.62036 (13268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7476 (pp20) cc_final: 0.7185 (pp20) REVERT: A 221 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: A 236 SER cc_start: 0.8456 (m) cc_final: 0.8248 (m) REVERT: A 418 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: A 493 ILE cc_start: 0.9198 (mm) cc_final: 0.8602 (tp) REVERT: A 495 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: A 550 TYR cc_start: 0.8132 (t80) cc_final: 0.7378 (t80) REVERT: A 558 LEU cc_start: 0.8304 (mt) cc_final: 0.7842 (tt) REVERT: A 605 ILE cc_start: 0.7140 (mm) cc_final: 0.6792 (mm) REVERT: A 874 ILE cc_start: 0.8948 (mt) cc_final: 0.8724 (mm) REVERT: A 887 ARG cc_start: 0.7874 (ptt90) cc_final: 0.7498 (ptt90) REVERT: A 1061 LEU cc_start: 0.8664 (tt) cc_final: 0.8325 (mm) REVERT: A 1069 GLU cc_start: 0.8204 (tp30) cc_final: 0.7977 (tp30) REVERT: A 1147 TRP cc_start: 0.8386 (m100) cc_final: 0.7800 (m100) REVERT: A 1201 ASP cc_start: 0.7610 (t0) cc_final: 0.7149 (t0) REVERT: A 1210 ARG cc_start: 0.8005 (ptt-90) cc_final: 0.7513 (tmm-80) REVERT: A 1235 LEU cc_start: 0.8828 (mt) cc_final: 0.8575 (tt) outliers start: 31 outliers final: 23 residues processed: 184 average time/residue: 0.2219 time to fit residues: 59.6088 Evaluate side-chains 178 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1244 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.0470 chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.131198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095070 restraints weight = 22310.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098017 restraints weight = 11802.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.099975 restraints weight = 7765.416| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9784 Z= 0.135 Angle : 0.630 10.635 13268 Z= 0.317 Chirality : 0.042 0.279 1538 Planarity : 0.004 0.040 1642 Dihedral : 5.621 51.436 1308 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.17 % Allowed : 18.71 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.25), residues: 1187 helix: 1.45 (0.18), residues: 780 sheet: 0.81 (0.55), residues: 79 loop : 0.59 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1147 HIS 0.006 0.001 HIS A1141 PHE 0.054 0.002 PHE A1269 TYR 0.035 0.002 TYR A 289 ARG 0.006 0.000 ARG A1114 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 634) hydrogen bonds : angle 4.44017 ( 1815) covalent geometry : bond 0.00298 ( 9784) covalent geometry : angle 0.62995 (13268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.255 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: A 61 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8453 (tp40) REVERT: A 103 GLU cc_start: 0.7473 (pp20) cc_final: 0.7198 (pp20) REVERT: A 126 MET cc_start: 0.7443 (mmp) cc_final: 0.6509 (tmm) REVERT: A 221 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: A 236 SER cc_start: 0.8418 (m) cc_final: 0.8209 (m) REVERT: A 418 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: A 493 ILE cc_start: 0.9195 (mm) cc_final: 0.8580 (tp) REVERT: A 495 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: A 550 TYR cc_start: 0.8127 (t80) cc_final: 0.7392 (t80) REVERT: A 558 LEU cc_start: 0.8277 (mt) cc_final: 0.7781 (tt) REVERT: A 605 ILE cc_start: 0.7116 (mm) cc_final: 0.6752 (mm) REVERT: A 887 ARG cc_start: 0.7844 (ptt90) cc_final: 0.7469 (ptt90) REVERT: A 990 MET cc_start: 0.8015 (tpp) cc_final: 0.7764 (tpp) REVERT: A 1061 LEU cc_start: 0.8653 (tt) cc_final: 0.8341 (mm) REVERT: A 1147 TRP cc_start: 0.8257 (m100) cc_final: 0.7572 (m100) REVERT: A 1201 ASP cc_start: 0.7565 (t0) cc_final: 0.7167 (t70) REVERT: A 1210 ARG cc_start: 0.7944 (ptt-90) cc_final: 0.7680 (tmm-80) REVERT: A 1269 PHE cc_start: 0.8683 (t80) cc_final: 0.8437 (t80) outliers start: 33 outliers final: 26 residues processed: 179 average time/residue: 0.2308 time to fit residues: 61.3653 Evaluate side-chains 176 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 82 optimal weight: 0.0000 chunk 6 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.130841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094482 restraints weight = 22238.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097430 restraints weight = 11829.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.099387 restraints weight = 7789.985| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9784 Z= 0.141 Angle : 0.634 11.080 13268 Z= 0.318 Chirality : 0.041 0.182 1538 Planarity : 0.004 0.040 1642 Dihedral : 5.567 53.493 1308 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.88 % Allowed : 19.48 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1187 helix: 1.44 (0.19), residues: 787 sheet: 1.05 (0.56), residues: 79 loop : 0.49 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 863 HIS 0.005 0.001 HIS A1141 PHE 0.033 0.002 PHE A1269 TYR 0.028 0.001 TYR A 289 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 634) hydrogen bonds : angle 4.43934 ( 1815) covalent geometry : bond 0.00318 ( 9784) covalent geometry : angle 0.63370 (13268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8484 (tp40) REVERT: A 103 GLU cc_start: 0.7506 (pp20) cc_final: 0.7267 (pp20) REVERT: A 126 MET cc_start: 0.7409 (mmp) cc_final: 0.6316 (tmm) REVERT: A 288 MET cc_start: 0.8574 (tpp) cc_final: 0.8214 (mmm) REVERT: A 418 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: A 493 ILE cc_start: 0.9190 (mm) cc_final: 0.8539 (tp) REVERT: A 550 TYR cc_start: 0.8155 (t80) cc_final: 0.7416 (t80) REVERT: A 558 LEU cc_start: 0.8260 (mt) cc_final: 0.7771 (tt) REVERT: A 605 ILE cc_start: 0.7164 (mm) cc_final: 0.6824 (mm) REVERT: A 887 ARG cc_start: 0.7864 (ptt90) cc_final: 0.7460 (ptt90) REVERT: A 990 MET cc_start: 0.8019 (tpp) cc_final: 0.7813 (tpp) REVERT: A 1061 LEU cc_start: 0.8665 (tt) cc_final: 0.8337 (mm) REVERT: A 1147 TRP cc_start: 0.8293 (m100) cc_final: 0.7759 (m100) REVERT: A 1201 ASP cc_start: 0.7562 (t0) cc_final: 0.7131 (t70) REVERT: A 1210 ARG cc_start: 0.8080 (ptt-90) cc_final: 0.7783 (tmm-80) REVERT: A 1234 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7917 (ptm160) outliers start: 30 outliers final: 25 residues processed: 176 average time/residue: 0.1880 time to fit residues: 48.5792 Evaluate side-chains 176 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 chunk 104 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.131312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095235 restraints weight = 22373.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098202 restraints weight = 11808.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100154 restraints weight = 7729.649| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9784 Z= 0.135 Angle : 0.644 10.560 13268 Z= 0.322 Chirality : 0.042 0.245 1538 Planarity : 0.004 0.040 1642 Dihedral : 5.535 57.103 1308 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.50 % Allowed : 20.44 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1187 helix: 1.40 (0.18), residues: 791 sheet: 1.08 (0.57), residues: 79 loop : 0.44 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1147 HIS 0.005 0.001 HIS A1141 PHE 0.019 0.001 PHE A 258 TYR 0.026 0.001 TYR A 289 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 634) hydrogen bonds : angle 4.42718 ( 1815) covalent geometry : bond 0.00300 ( 9784) covalent geometry : angle 0.64391 (13268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8477 (tp40) REVERT: A 103 GLU cc_start: 0.7468 (pp20) cc_final: 0.7222 (pp20) REVERT: A 126 MET cc_start: 0.7299 (mmp) cc_final: 0.6247 (tmm) REVERT: A 288 MET cc_start: 0.8581 (tpp) cc_final: 0.8222 (mmm) REVERT: A 418 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7223 (m-80) REVERT: A 493 ILE cc_start: 0.9295 (mm) cc_final: 0.8805 (tp) REVERT: A 550 TYR cc_start: 0.8175 (t80) cc_final: 0.7504 (t80) REVERT: A 558 LEU cc_start: 0.8298 (mt) cc_final: 0.7791 (tt) REVERT: A 605 ILE cc_start: 0.7215 (mm) cc_final: 0.6897 (mm) REVERT: A 887 ARG cc_start: 0.7842 (ptt90) cc_final: 0.7462 (ptt90) REVERT: A 1061 LEU cc_start: 0.8662 (tt) cc_final: 0.8346 (mm) REVERT: A 1147 TRP cc_start: 0.8230 (m100) cc_final: 0.7647 (m100) REVERT: A 1157 GLU cc_start: 0.8645 (mp0) cc_final: 0.8294 (pp20) REVERT: A 1201 ASP cc_start: 0.7527 (t0) cc_final: 0.7130 (t70) REVERT: A 1210 ARG cc_start: 0.8014 (ptt-90) cc_final: 0.7765 (tmm-80) outliers start: 26 outliers final: 23 residues processed: 170 average time/residue: 0.2138 time to fit residues: 54.3801 Evaluate side-chains 172 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1230 THR Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 chunk 3 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.131923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095720 restraints weight = 22025.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098666 restraints weight = 11752.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100621 restraints weight = 7768.887| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9784 Z= 0.141 Angle : 0.675 13.687 13268 Z= 0.335 Chirality : 0.042 0.206 1538 Planarity : 0.004 0.040 1642 Dihedral : 5.522 59.854 1308 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.59 % Allowed : 20.73 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1187 helix: 1.42 (0.18), residues: 790 sheet: 1.11 (0.57), residues: 80 loop : 0.44 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1147 HIS 0.005 0.001 HIS A1141 PHE 0.028 0.002 PHE A1048 TYR 0.027 0.001 TYR A 289 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 634) hydrogen bonds : angle 4.47303 ( 1815) covalent geometry : bond 0.00313 ( 9784) covalent geometry : angle 0.67461 (13268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3630.09 seconds wall clock time: 65 minutes 19.69 seconds (3919.69 seconds total)