Starting phenix.real_space_refine on Fri Feb 14 05:49:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz8_35835/02_2025/8iz8_35835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz8_35835/02_2025/8iz8_35835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iz8_35835/02_2025/8iz8_35835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz8_35835/02_2025/8iz8_35835.map" model { file = "/net/cci-nas-00/data/ceres_data/8iz8_35835/02_2025/8iz8_35835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz8_35835/02_2025/8iz8_35835.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.060 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 44 5.16 5 C 6366 2.51 5 N 1645 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9805 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9805 Classifications: {'peptide': 1230} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1190} Chain breaks: 2 Time building chain proxies: 6.00, per 1000 atoms: 0.61 Number of scatterers: 9805 At special positions: 0 Unit cell: (83.888, 106.144, 145.52, 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 44 16.00 O 1750 8.00 N 1645 7.00 C 6366 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 70.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.847A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.700A pdb=" N MET A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.623A pdb=" N LEU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.030A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 4.066A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 122 removed outlier: 4.410A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.582A pdb=" N TYR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 179 removed outlier: 3.796A pdb=" N LEU A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N HIS A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.748A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.935A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 282 removed outlier: 4.613A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.791A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 343 removed outlier: 3.934A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 368 Processing helix chain 'A' and resid 368 through 391 Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 529 through 533 removed outlier: 4.336A pdb=" N GLY A 532 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR A 533 " --> pdb=" O ASP A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 533' Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.689A pdb=" N GLN A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 582 removed outlier: 4.941A pdb=" N CYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.888A pdb=" N LEU A 597 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 598' Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 626 through 631 removed outlier: 3.903A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 4.085A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 751 removed outlier: 3.998A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.962A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 834 removed outlier: 3.621A pdb=" N ILE A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 861 removed outlier: 4.018A pdb=" N LEU A 838 " --> pdb=" O ASP A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 866 removed outlier: 3.790A pdb=" N ALA A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 866 " --> pdb=" O TRP A 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 862 through 866' Processing helix chain 'A' and resid 867 through 910 removed outlier: 3.602A pdb=" N LEU A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.029A 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 removed outlier: 3.552A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 970 removed outlier: 3.711A pdb=" N CYS A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 988 through 1007 removed outlier: 4.143A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1018 removed outlier: 3.717A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1090 Processing helix chain 'A' and resid 1110 through 1115 removed outlier: 3.747A pdb=" N LYS A1115 " --> pdb=" O HIS A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 removed outlier: 3.686A pdb=" N VAL A1153 " --> pdb=" O ALA A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 3.512A pdb=" N ILE A1159 " --> pdb=" O LEU A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1175 removed outlier: 3.520A pdb=" N SER A1175 " --> pdb=" O GLU A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1208 through 1222 Processing helix chain 'A' and resid 1257 through 1263 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1277 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.003A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA A 442 " --> pdb=" O LEU A 604 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 477 through 478 Processing sheet with id=AA3, first strand: chain 'A' and resid 1041 through 1044 removed outlier: 3.557A pdb=" N ASP A1044 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS A1097 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1229 through 1232 removed outlier: 7.124A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA A1232 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A1073 " --> pdb=" O ALA A1232 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS A1253 " --> pdb=" O VAL A1246 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1833 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: 3.23 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3108 1.34 - 1.46: 2233 1.46 - 1.58: 4602 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 10015 Sorted by residual: bond pdb=" C ILE A 866 " pdb=" N PRO A 867 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 6.96e+00 bond pdb=" CA VAL A 527 " pdb=" CB VAL A 527 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 8.13e-01 bond pdb=" CA VAL A 755 " pdb=" CB VAL A 755 " ideal model delta sigma weight residual 1.547 1.533 0.014 1.68e-02 3.54e+03 6.84e-01 bond pdb=" N ASP A 414 " pdb=" CA ASP A 414 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.54e-02 4.22e+03 6.00e-01 bond pdb=" CA ARG A 531 " pdb=" CB ARG A 531 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.95e-01 ... (remaining 10010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 13150 1.26 - 2.52: 360 2.52 - 3.78: 46 3.78 - 5.04: 12 5.04 - 6.30: 7 Bond angle restraints: 13575 Sorted by residual: angle pdb=" C ASP A 530 " pdb=" N ARG A 531 " pdb=" CA ARG A 531 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N GLU A1107 " pdb=" CA GLU A1107 " pdb=" C GLU A1107 " ideal model delta sigma weight residual 114.12 110.54 3.58 1.39e+00 5.18e-01 6.64e+00 angle pdb=" C GLN A 413 " pdb=" N ASP A 414 " pdb=" CA ASP A 414 " ideal model delta sigma weight residual 122.46 125.45 -2.99 1.41e+00 5.03e-01 4.50e+00 angle pdb=" C ASP A1161 " pdb=" N LEU A1162 " pdb=" CA LEU A1162 " ideal model delta sigma weight residual 120.68 123.61 -2.93 1.52e+00 4.33e-01 3.72e+00 angle pdb=" C ILE A 866 " pdb=" N PRO A 867 " pdb=" CA PRO A 867 " ideal model delta sigma weight residual 120.83 118.87 1.96 1.02e+00 9.61e-01 3.69e+00 ... (remaining 13570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5378 17.96 - 35.93: 489 35.93 - 53.89: 94 53.89 - 71.85: 9 71.85 - 89.82: 9 Dihedral angle restraints: 5979 sinusoidal: 2389 harmonic: 3590 Sorted by residual: dihedral pdb=" CA GLU A 7 " pdb=" C GLU A 7 " pdb=" N VAL A 8 " pdb=" CA VAL A 8 " ideal model delta harmonic sigma weight residual -180.00 -159.19 -20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CB GLU A 278 " pdb=" CG GLU A 278 " pdb=" CD GLU A 278 " pdb=" OE1 GLU A 278 " ideal model delta sinusoidal sigma weight residual 0.00 87.94 -87.94 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 693 " pdb=" CG GLU A 693 " pdb=" CD GLU A 693 " pdb=" OE1 GLU A 693 " ideal model delta sinusoidal sigma weight residual 0.00 -86.84 86.84 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 5976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1102 0.033 - 0.066: 344 0.066 - 0.099: 95 0.099 - 0.132: 35 0.132 - 0.165: 1 Chirality restraints: 1577 Sorted by residual: chirality pdb=" CB VAL A1153 " pdb=" CA VAL A1153 " pdb=" CG1 VAL A1153 " pdb=" CG2 VAL A1153 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB THR A1106 " pdb=" CA THR A1106 " pdb=" OG1 THR A1106 " pdb=" CG2 THR A1106 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A1120 " pdb=" N ILE A1120 " pdb=" C ILE A1120 " pdb=" CB ILE A1120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1574 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 898 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 899 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1208 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A1209 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A1209 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1209 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 9 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A 10 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " 0.018 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2349 2.79 - 3.32: 9534 3.32 - 3.85: 16344 3.85 - 4.37: 17935 4.37 - 4.90: 31545 Nonbonded interactions: 77707 Sorted by model distance: nonbonded pdb=" O LEU A1064 " pdb=" OH TYR A1255 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU A 121 " pdb=" OG1 THR A 347 " model vdw 2.301 3.040 nonbonded pdb=" OG SER A 804 " pdb=" O TYR A1016 " model vdw 2.310 3.040 nonbonded pdb=" O LEU A 181 " pdb=" NH1 ARG A 915 " model vdw 2.320 3.120 nonbonded pdb=" O HIS A 411 " pdb=" OG SER A 470 " model vdw 2.335 3.040 ... (remaining 77702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 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 : 0.002 0.022 10015 Z= 0.117 Angle : 0.496 6.300 13575 Z= 0.302 Chirality : 0.036 0.165 1577 Planarity : 0.003 0.036 1688 Dihedral : 14.068 89.818 3655 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.97 (0.23), residues: 1224 helix: 0.18 (0.17), residues: 799 sheet: -1.70 (0.75), residues: 45 loop : -2.19 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP A 763 HIS 0.002 0.000 HIS A1225 PHE 0.008 0.001 PHE A 495 TYR 0.007 0.001 TYR A 339 ARG 0.002 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8260 (tt) cc_final: 0.7950 (mp) REVERT: A 91 SER cc_start: 0.8073 (m) cc_final: 0.7836 (p) REVERT: A 118 ASN cc_start: 0.8240 (t0) cc_final: 0.8019 (t0) REVERT: A 211 PHE cc_start: 0.8072 (m-80) cc_final: 0.7808 (m-80) REVERT: A 273 ILE cc_start: 0.8504 (mm) cc_final: 0.8303 (mt) REVERT: A 363 LEU cc_start: 0.8310 (tp) cc_final: 0.8076 (mt) REVERT: A 811 LEU cc_start: 0.8248 (tp) cc_final: 0.7852 (mt) REVERT: A 1029 LYS cc_start: 0.7170 (ttpt) cc_final: 0.6879 (pttt) REVERT: A 1131 MET cc_start: 0.7298 (tpt) cc_final: 0.7093 (tpt) REVERT: A 1133 LYS cc_start: 0.6963 (tmtt) cc_final: 0.6500 (tptt) REVERT: A 1183 GLN cc_start: 0.7485 (tt0) cc_final: 0.7168 (mt0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2831 time to fit residues: 70.7229 Evaluate side-chains 107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 480 GLN A 613 GLN A 710 HIS A 725 GLN A 754 ASN A 903 HIS A 931 GLN A1141 HIS A1183 GLN A1225 HIS A1290 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.207488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140852 restraints weight = 12081.559| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.55 r_work: 0.3582 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10015 Z= 0.245 Angle : 0.579 14.613 13575 Z= 0.291 Chirality : 0.041 0.171 1577 Planarity : 0.004 0.037 1688 Dihedral : 3.446 21.151 1326 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.21 % Allowed : 11.76 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.21 (0.24), residues: 1224 helix: 0.98 (0.18), residues: 811 sheet: -1.06 (0.75), residues: 48 loop : -1.56 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.008 0.002 HIS A 153 PHE 0.027 0.002 PHE A1089 TYR 0.014 0.002 TYR A 157 ARG 0.005 0.001 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.240 Fit side-chains REVERT: A 164 MET cc_start: 0.8602 (tmm) cc_final: 0.8319 (ttp) REVERT: A 246 ILE cc_start: 0.8228 (tt) cc_final: 0.7581 (mt) REVERT: A 409 MET cc_start: 0.3349 (mmt) cc_final: 0.3138 (mmp) REVERT: A 706 ARG cc_start: 0.7802 (ttt180) cc_final: 0.7386 (mmt-90) REVERT: A 965 PHE cc_start: 0.6541 (m-10) cc_final: 0.6192 (m-80) REVERT: A 1029 LYS cc_start: 0.7432 (ttpt) cc_final: 0.6702 (pttp) REVERT: A 1133 LYS cc_start: 0.7239 (tmtt) cc_final: 0.6649 (tptt) REVERT: A 1230 THR cc_start: 0.7648 (p) cc_final: 0.7374 (p) outliers start: 13 outliers final: 7 residues processed: 133 average time/residue: 0.2483 time to fit residues: 45.9113 Evaluate side-chains 107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 GLN A 931 GLN A1183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.207797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141592 restraints weight = 12273.158| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.51 r_work: 0.3602 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10015 Z= 0.164 Angle : 0.488 14.285 13575 Z= 0.241 Chirality : 0.039 0.135 1577 Planarity : 0.003 0.038 1688 Dihedral : 3.256 21.346 1326 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.49 % Allowed : 15.31 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.91 (0.24), residues: 1224 helix: 1.51 (0.18), residues: 814 sheet: -0.63 (0.77), residues: 48 loop : -1.30 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.006 0.001 HIS A 153 PHE 0.017 0.001 PHE A 336 TYR 0.011 0.001 TYR A 157 ARG 0.004 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6980 (mp0) REVERT: A 246 ILE cc_start: 0.8281 (tt) cc_final: 0.7765 (mt) REVERT: A 262 ARG cc_start: 0.7454 (tpp-160) cc_final: 0.6862 (mmt-90) REVERT: A 706 ARG cc_start: 0.7618 (ttt180) cc_final: 0.7272 (mmt-90) REVERT: A 744 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7503 (mtp) REVERT: A 909 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7435 (mm-40) REVERT: A 1029 LYS cc_start: 0.7563 (ttpt) cc_final: 0.6900 (pttp) REVERT: A 1133 LYS cc_start: 0.7090 (tmtt) cc_final: 0.6556 (tptt) REVERT: A 1183 GLN cc_start: 0.7538 (tp40) cc_final: 0.7310 (tp-100) REVERT: A 1192 LEU cc_start: 0.7176 (tt) cc_final: 0.6946 (tt) REVERT: A 1230 THR cc_start: 0.7439 (p) cc_final: 0.7212 (p) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 0.2332 time to fit residues: 40.2267 Evaluate side-chains 105 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1275 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 48 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.206080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139613 restraints weight = 12139.171| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.56 r_work: 0.3575 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10015 Z= 0.165 Angle : 0.490 14.585 13575 Z= 0.240 Chirality : 0.038 0.133 1577 Planarity : 0.003 0.038 1688 Dihedral : 3.271 21.679 1326 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.15 % Allowed : 15.50 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.24 (0.25), residues: 1224 helix: 1.70 (0.18), residues: 815 sheet: 0.44 (0.84), residues: 42 loop : -1.14 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.006 0.001 HIS A 153 PHE 0.018 0.001 PHE A 336 TYR 0.010 0.001 TYR A 881 ARG 0.005 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.064 Fit side-chains REVERT: A 58 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6945 (mp0) REVERT: A 241 MET cc_start: 0.8937 (mmm) cc_final: 0.8699 (mmm) REVERT: A 246 ILE cc_start: 0.8363 (tt) cc_final: 0.7886 (mt) REVERT: A 706 ARG cc_start: 0.7711 (ttt180) cc_final: 0.7358 (mmt-90) REVERT: A 744 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7518 (mtp) REVERT: A 909 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7420 (mm-40) REVERT: A 1029 LYS cc_start: 0.7785 (ttpt) cc_final: 0.6914 (pttp) REVERT: A 1133 LYS cc_start: 0.7214 (tmtt) cc_final: 0.6653 (tptt) REVERT: A 1183 GLN cc_start: 0.7539 (tp40) cc_final: 0.7112 (tp-100) REVERT: A 1230 THR cc_start: 0.7332 (p) cc_final: 0.7084 (p) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.2232 time to fit residues: 37.6141 Evaluate side-chains 109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1193 ARG Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.204088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142030 restraints weight = 11992.180| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.43 r_work: 0.3536 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10015 Z= 0.171 Angle : 0.493 14.172 13575 Z= 0.244 Chirality : 0.039 0.134 1577 Planarity : 0.003 0.037 1688 Dihedral : 3.307 22.843 1326 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.77 % Allowed : 17.09 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.36 (0.25), residues: 1224 helix: 1.76 (0.18), residues: 814 sheet: 0.68 (0.87), residues: 42 loop : -1.03 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.006 0.001 HIS A 153 PHE 0.019 0.001 PHE A 336 TYR 0.011 0.001 TYR A 881 ARG 0.005 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.067 Fit side-chains REVERT: A 58 GLU cc_start: 0.7636 (mt-10) cc_final: 0.6889 (mp0) REVERT: A 90 LYS cc_start: 0.8369 (pttt) cc_final: 0.8161 (tptp) REVERT: A 241 MET cc_start: 0.8945 (mmm) cc_final: 0.8719 (mmm) REVERT: A 246 ILE cc_start: 0.8413 (tt) cc_final: 0.7978 (mt) REVERT: A 555 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7679 (mp) REVERT: A 706 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7401 (mmt-90) REVERT: A 744 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7648 (mtp) REVERT: A 909 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7409 (mm-40) REVERT: A 1133 LYS cc_start: 0.7139 (tmtt) cc_final: 0.6565 (tptt) REVERT: A 1150 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7651 (mm) REVERT: A 1183 GLN cc_start: 0.7592 (tp40) cc_final: 0.7179 (tp-100) REVERT: A 1230 THR cc_start: 0.7261 (p) cc_final: 0.7020 (p) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.2110 time to fit residues: 34.1996 Evaluate side-chains 108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 903 HIS A1151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.203688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137905 restraints weight = 12059.530| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.49 r_work: 0.3559 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10015 Z= 0.163 Angle : 0.481 13.900 13575 Z= 0.238 Chirality : 0.038 0.134 1577 Planarity : 0.003 0.037 1688 Dihedral : 3.309 22.560 1326 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.24 % Allowed : 17.18 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1224 helix: 1.82 (0.18), residues: 815 sheet: 0.04 (0.91), residues: 38 loop : -0.80 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.005 0.001 HIS A 153 PHE 0.017 0.001 PHE A 336 TYR 0.011 0.001 TYR A1016 ARG 0.004 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.201 Fit side-chains REVERT: A 90 LYS cc_start: 0.8435 (pttt) cc_final: 0.8131 (ttpt) REVERT: A 173 MET cc_start: 0.9157 (mtp) cc_final: 0.8780 (mtp) REVERT: A 246 ILE cc_start: 0.8409 (tt) cc_final: 0.7993 (mt) REVERT: A 555 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7972 (mp) REVERT: A 706 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7408 (mmt-90) REVERT: A 744 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7776 (mtp) REVERT: A 909 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7492 (mm-40) REVERT: A 1133 LYS cc_start: 0.7268 (tmtt) cc_final: 0.6684 (tptt) REVERT: A 1183 GLN cc_start: 0.7707 (tp40) cc_final: 0.7279 (tp-100) REVERT: A 1230 THR cc_start: 0.7615 (p) cc_final: 0.7366 (p) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.2298 time to fit residues: 37.8525 Evaluate side-chains 109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 89 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.204099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138559 restraints weight = 12144.305| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.56 r_work: 0.3561 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10015 Z= 0.145 Angle : 0.476 13.927 13575 Z= 0.233 Chirality : 0.038 0.146 1577 Planarity : 0.003 0.037 1688 Dihedral : 3.268 22.602 1326 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.49 % Allowed : 18.11 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.62 (0.25), residues: 1224 helix: 1.91 (0.18), residues: 816 sheet: 0.17 (0.91), residues: 38 loop : -0.73 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.005 0.001 HIS A 153 PHE 0.016 0.001 PHE A 143 TYR 0.014 0.001 TYR A1016 ARG 0.004 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 246 ILE cc_start: 0.8428 (tt) cc_final: 0.8016 (mt) REVERT: A 555 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7836 (mp) REVERT: A 706 ARG cc_start: 0.7835 (ttt180) cc_final: 0.7410 (tpp-160) REVERT: A 744 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7603 (mtp) REVERT: A 1018 ASP cc_start: 0.7156 (m-30) cc_final: 0.6812 (m-30) REVERT: A 1024 PRO cc_start: 0.8018 (Cg_exo) cc_final: 0.7805 (Cg_endo) REVERT: A 1133 LYS cc_start: 0.7189 (tmtt) cc_final: 0.6559 (tptt) REVERT: A 1150 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7645 (mm) REVERT: A 1183 GLN cc_start: 0.7582 (tp40) cc_final: 0.7177 (tp-100) REVERT: A 1230 THR cc_start: 0.7210 (p) cc_final: 0.6961 (p) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.2180 time to fit residues: 35.7648 Evaluate side-chains 105 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.202103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136922 restraints weight = 12188.666| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.50 r_work: 0.3547 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10015 Z= 0.166 Angle : 0.501 14.123 13575 Z= 0.244 Chirality : 0.039 0.144 1577 Planarity : 0.003 0.037 1688 Dihedral : 3.387 22.620 1326 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.05 % Allowed : 18.49 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.59 (0.25), residues: 1224 helix: 1.85 (0.18), residues: 817 sheet: 0.24 (0.90), residues: 38 loop : -0.63 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.005 0.001 HIS A 153 PHE 0.017 0.001 PHE A 336 TYR 0.013 0.001 TYR A1016 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.146 Fit side-chains REVERT: A 173 MET cc_start: 0.9115 (mtp) cc_final: 0.8745 (mtp) REVERT: A 246 ILE cc_start: 0.8424 (tt) cc_final: 0.8011 (mt) REVERT: A 474 ARG cc_start: 0.7592 (mmm160) cc_final: 0.7367 (mtp180) REVERT: A 706 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7575 (tpp-160) REVERT: A 744 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7727 (mtp) REVERT: A 1018 ASP cc_start: 0.7316 (m-30) cc_final: 0.6990 (m-30) REVERT: A 1024 PRO cc_start: 0.8080 (Cg_exo) cc_final: 0.7862 (Cg_endo) REVERT: A 1133 LYS cc_start: 0.7282 (tmtt) cc_final: 0.6666 (tptt) REVERT: A 1150 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7739 (mm) REVERT: A 1183 GLN cc_start: 0.7699 (tp40) cc_final: 0.7288 (tp-100) REVERT: A 1222 LYS cc_start: 0.7106 (tptp) cc_final: 0.6701 (mmtm) REVERT: A 1230 THR cc_start: 0.7641 (p) cc_final: 0.7393 (p) outliers start: 22 outliers final: 16 residues processed: 117 average time/residue: 0.2335 time to fit residues: 39.5628 Evaluate side-chains 118 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 79 optimal weight: 0.0870 chunk 50 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.200096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134855 restraints weight = 12151.385| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.50 r_work: 0.3525 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10015 Z= 0.190 Angle : 0.521 13.780 13575 Z= 0.256 Chirality : 0.039 0.137 1577 Planarity : 0.003 0.035 1688 Dihedral : 3.466 23.485 1326 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.15 % Allowed : 18.95 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.50 (0.25), residues: 1224 helix: 1.78 (0.18), residues: 817 sheet: -0.59 (0.79), residues: 49 loop : -0.55 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.006 0.001 HIS A 153 PHE 0.019 0.001 PHE A 336 TYR 0.012 0.001 TYR A1016 ARG 0.004 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8499 (pttt) cc_final: 0.8200 (ttpt) REVERT: A 173 MET cc_start: 0.9173 (mtp) cc_final: 0.8812 (mtp) REVERT: A 246 ILE cc_start: 0.8414 (tt) cc_final: 0.8059 (mt) REVERT: A 288 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7651 (mtt) REVERT: A 706 ARG cc_start: 0.8094 (ttt180) cc_final: 0.7638 (tpp-160) REVERT: A 744 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7722 (mtp) REVERT: A 1018 ASP cc_start: 0.7311 (m-30) cc_final: 0.6979 (m-30) REVERT: A 1133 LYS cc_start: 0.7368 (tmtt) cc_final: 0.6704 (tptt) REVERT: A 1150 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 1183 GLN cc_start: 0.7728 (tp40) cc_final: 0.7331 (tp-100) REVERT: A 1221 GLU cc_start: 0.6889 (pt0) cc_final: 0.5846 (tm-30) REVERT: A 1230 THR cc_start: 0.7758 (p) cc_final: 0.7513 (p) outliers start: 23 outliers final: 17 residues processed: 121 average time/residue: 0.2031 time to fit residues: 35.7140 Evaluate side-chains 121 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.200858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143304 restraints weight = 12108.447| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.55 r_work: 0.3531 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10015 Z= 0.169 Angle : 0.514 13.311 13575 Z= 0.252 Chirality : 0.039 0.140 1577 Planarity : 0.003 0.036 1688 Dihedral : 3.464 23.389 1326 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.96 % Allowed : 18.86 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.59 (0.25), residues: 1224 helix: 1.85 (0.18), residues: 817 sheet: -0.60 (0.81), residues: 49 loop : -0.50 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.005 0.001 HIS A 153 PHE 0.017 0.001 PHE A 143 TYR 0.011 0.001 TYR A1016 ARG 0.004 0.000 ARG A 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8359 (pttt) cc_final: 0.8043 (ttpt) REVERT: A 173 MET cc_start: 0.8882 (mtp) cc_final: 0.8508 (mtp) REVERT: A 246 ILE cc_start: 0.8279 (tt) cc_final: 0.7940 (mt) REVERT: A 262 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.6933 (mmt180) REVERT: A 288 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7620 (mtm) REVERT: A 706 ARG cc_start: 0.7772 (ttt180) cc_final: 0.7355 (tpp-160) REVERT: A 744 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7377 (mtp) REVERT: A 834 ASP cc_start: 0.8242 (m-30) cc_final: 0.8041 (m-30) REVERT: A 1018 ASP cc_start: 0.7067 (m-30) cc_final: 0.6709 (m-30) REVERT: A 1133 LYS cc_start: 0.7057 (tmtt) cc_final: 0.6423 (tptt) REVERT: A 1150 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7605 (mm) REVERT: A 1183 GLN cc_start: 0.7565 (tp40) cc_final: 0.7160 (tp-100) REVERT: A 1221 GLU cc_start: 0.6785 (pt0) cc_final: 0.5617 (tm-30) REVERT: A 1222 LYS cc_start: 0.7575 (tppt) cc_final: 0.6596 (mmtm) REVERT: A 1230 THR cc_start: 0.7248 (p) cc_final: 0.7008 (p) outliers start: 21 outliers final: 15 residues processed: 117 average time/residue: 0.2261 time to fit residues: 38.0401 Evaluate side-chains 117 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.201311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136570 restraints weight = 11999.797| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.49 r_work: 0.3529 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10015 Z= 0.144 Angle : 0.505 13.662 13575 Z= 0.244 Chirality : 0.038 0.139 1577 Planarity : 0.003 0.036 1688 Dihedral : 3.364 22.649 1326 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.96 % Allowed : 19.14 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.72 (0.25), residues: 1224 helix: 1.94 (0.18), residues: 819 sheet: 0.35 (0.91), residues: 38 loop : -0.57 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.004 0.001 HIS A 153 PHE 0.017 0.001 PHE A 143 TYR 0.010 0.001 TYR A1016 ARG 0.007 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5311.87 seconds wall clock time: 94 minutes 54.34 seconds (5694.34 seconds total)