Starting phenix.real_space_refine on Wed Apr 30 19:35:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz8_35835/04_2025/8iz8_35835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz8_35835/04_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_35835/04_2025/8iz8_35835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz8_35835/04_2025/8iz8_35835.map" model { file = "/net/cci-nas-00/data/ceres_data/8iz8_35835/04_2025/8iz8_35835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz8_35835/04_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-5669/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: 5.79, per 1000 atoms: 0.59 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 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: 1.17 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: 3.08 Time building geometry restraints manager: 2.80 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.090 Process input model: 24.430 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- 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= 0.116 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 Details of bonding type rmsd hydrogen bonds : bond 0.13955 ( 616) hydrogen bonds : angle 5.10237 ( 1833) covalent geometry : bond 0.00185 (10015) covalent geometry : angle 0.49608 (13575) *********************** 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 : 1.071 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: 0.2727 time to fit residues: 68.0733 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 : 1.077 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140950 restraints weight = 12081.560| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.53 r_work: 0.3583 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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= 0.173 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 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 616) hydrogen bonds : angle 4.06564 ( 1833) covalent geometry : bond 0.00381 (10015) covalent geometry : angle 0.57909 (13575) *********************** 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 : 1.172 Fit side-chains REVERT: A 164 MET cc_start: 0.8604 (tmm) cc_final: 0.8319 (ttp) REVERT: A 246 ILE cc_start: 0.8231 (tt) cc_final: 0.7583 (mt) REVERT: A 409 MET cc_start: 0.3352 (mmt) cc_final: 0.3141 (mmp) REVERT: A 706 ARG cc_start: 0.7792 (ttt180) cc_final: 0.7389 (mmt-90) REVERT: A 965 PHE cc_start: 0.6540 (m-10) cc_final: 0.6192 (m-80) REVERT: A 1029 LYS cc_start: 0.7437 (ttpt) cc_final: 0.6706 (pttp) REVERT: A 1133 LYS cc_start: 0.7235 (tmtt) cc_final: 0.6645 (tptt) REVERT: A 1230 THR cc_start: 0.7633 (p) cc_final: 0.7359 (p) outliers start: 13 outliers final: 7 residues processed: 133 average time/residue: 0.2887 time to fit residues: 54.6394 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 : 1.196 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 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: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4424 r_free = 0.4424 target = 0.206166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139403 restraints weight = 12273.462| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.53 r_work: 0.3578 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10015 Z= 0.129 Angle : 0.500 14.405 13575 Z= 0.248 Chirality : 0.039 0.137 1577 Planarity : 0.003 0.037 1688 Dihedral : 3.322 21.736 1326 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.59 % Allowed : 15.22 % 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: 0.85 (0.24), residues: 1224 helix: 1.47 (0.18), residues: 812 sheet: -0.61 (0.77), residues: 48 loop : -1.33 (0.33), residues: 364 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 0.013 0.001 TYR A 157 ARG 0.004 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 616) hydrogen bonds : angle 3.78619 ( 1833) covalent geometry : bond 0.00297 (10015) covalent geometry : angle 0.50006 (13575) *********************** 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 127 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6977 (mp0) REVERT: A 246 ILE cc_start: 0.8327 (tt) cc_final: 0.7833 (mt) REVERT: A 706 ARG cc_start: 0.7652 (ttt180) cc_final: 0.7309 (mmt-90) REVERT: A 744 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7525 (mtp) REVERT: A 909 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7433 (mm-40) REVERT: A 965 PHE cc_start: 0.7444 (m-10) cc_final: 0.7009 (m-80) REVERT: A 1029 LYS cc_start: 0.7567 (ttpt) cc_final: 0.6856 (pttp) REVERT: A 1133 LYS cc_start: 0.7148 (tmtt) cc_final: 0.6602 (tptt) REVERT: A 1183 GLN cc_start: 0.7539 (tp40) cc_final: 0.7293 (tp-100) REVERT: A 1230 THR cc_start: 0.7485 (p) cc_final: 0.7270 (p) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.2663 time to fit residues: 47.2185 Evaluate side-chains 109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 159 VAL 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 1071 VAL 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: 2.9990 chunk 93 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 172 HIS A 183 ASN A 903 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.197307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138162 restraints weight = 12143.089| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.76 r_work: 0.3466 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10015 Z= 0.197 Angle : 0.597 12.907 13575 Z= 0.299 Chirality : 0.042 0.147 1577 Planarity : 0.004 0.047 1688 Dihedral : 3.807 25.421 1326 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.43 % Allowed : 15.78 % Favored : 81.79 % 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: 0.67 (0.24), residues: 1224 helix: 1.25 (0.18), residues: 811 sheet: -0.13 (0.79), residues: 48 loop : -1.26 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 947 HIS 0.013 0.001 HIS A 153 PHE 0.028 0.002 PHE A 336 TYR 0.014 0.001 TYR A 881 ARG 0.005 0.001 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.05052 ( 616) hydrogen bonds : angle 4.07239 ( 1833) covalent geometry : bond 0.00462 (10015) covalent geometry : angle 0.59657 (13575) *********************** 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 134 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.008 Fit side-chains REVERT: A 246 ILE cc_start: 0.8327 (tt) cc_final: 0.8100 (mt) REVERT: A 555 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7748 (mp) REVERT: A 706 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7408 (mmt-90) REVERT: A 744 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7605 (mtp) REVERT: A 909 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7510 (mm-40) REVERT: A 1130 THR cc_start: 0.7411 (p) cc_final: 0.7170 (p) REVERT: A 1133 LYS cc_start: 0.7229 (tmtt) cc_final: 0.6582 (tptt) REVERT: A 1151 GLN cc_start: 0.8780 (tp40) cc_final: 0.8548 (tp-100) REVERT: A 1154 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7272 (mm-40) REVERT: A 1183 GLN cc_start: 0.7588 (tp40) cc_final: 0.7106 (tp-100) REVERT: A 1222 LYS cc_start: 0.7223 (tptp) cc_final: 0.6767 (mmtm) REVERT: A 1230 THR cc_start: 0.7814 (p) cc_final: 0.7596 (p) outliers start: 26 outliers final: 16 residues processed: 127 average time/residue: 0.2264 time to fit residues: 41.0407 Evaluate side-chains 113 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 323 SER 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 909 GLN Chi-restraints excluded: chain A residue 1005 ASN 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: 0.9980 chunk 98 optimal weight: 0.9980 chunk 1 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.200487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135154 restraints weight = 11978.350| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.47 r_work: 0.3524 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5147 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= 0.122 Angle : 0.494 11.990 13575 Z= 0.247 Chirality : 0.039 0.137 1577 Planarity : 0.003 0.036 1688 Dihedral : 3.502 25.598 1326 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.43 % Allowed : 17.09 % Favored : 80.49 % 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: 1.09 (0.24), residues: 1224 helix: 1.54 (0.18), residues: 813 sheet: 0.08 (0.93), residues: 38 loop : -1.00 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 947 HIS 0.004 0.001 HIS A 153 PHE 0.017 0.001 PHE A 336 TYR 0.011 0.001 TYR A 123 ARG 0.006 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 616) hydrogen bonds : angle 3.78450 ( 1833) covalent geometry : bond 0.00273 (10015) covalent geometry : angle 0.49442 (13575) *********************** 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 130 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 246 ILE cc_start: 0.8471 (tt) cc_final: 0.8205 (mt) REVERT: A 474 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7502 (mtp180) REVERT: A 555 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7999 (mp) REVERT: A 706 ARG cc_start: 0.8045 (ttt180) cc_final: 0.7449 (mmt-90) REVERT: A 744 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7815 (mtp) REVERT: A 909 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7542 (mm-40) REVERT: A 931 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: A 1024 PRO cc_start: 0.8140 (Cg_exo) cc_final: 0.7923 (Cg_endo) REVERT: A 1070 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7743 (mmtm) REVERT: A 1133 LYS cc_start: 0.7368 (tmtt) cc_final: 0.6740 (tptt) REVERT: A 1183 GLN cc_start: 0.7763 (tp40) cc_final: 0.7301 (tp-100) REVERT: A 1193 ARG cc_start: 0.7214 (tpp80) cc_final: 0.6954 (ttm170) REVERT: A 1221 GLU cc_start: 0.6895 (pt0) cc_final: 0.5768 (tm-30) REVERT: A 1230 THR cc_start: 0.7788 (p) cc_final: 0.7570 (p) outliers start: 26 outliers final: 11 residues processed: 123 average time/residue: 0.2533 time to fit residues: 44.1621 Evaluate side-chains 116 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 159 VAL 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 909 GLN Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1192 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: 1.9990 chunk 118 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.199857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134596 restraints weight = 12024.047| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.50 r_work: 0.3517 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10015 Z= 0.123 Angle : 0.501 12.499 13575 Z= 0.249 Chirality : 0.039 0.214 1577 Planarity : 0.003 0.036 1688 Dihedral : 3.487 25.126 1326 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.61 % Allowed : 17.65 % Favored : 79.74 % 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: 1.64 (0.18), residues: 814 sheet: 0.47 (0.85), residues: 48 loop : -1.00 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 A 881 ARG 0.008 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 616) hydrogen bonds : angle 3.73174 ( 1833) covalent geometry : bond 0.00278 (10015) covalent geometry : angle 0.50147 (13575) *********************** 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 134 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.9146 (mtp) cc_final: 0.8769 (mtp) REVERT: A 246 ILE cc_start: 0.8445 (tt) cc_final: 0.8129 (mt) REVERT: A 706 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7594 (tpp-160) REVERT: A 744 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7757 (mtp) REVERT: A 909 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7543 (mm-40) REVERT: A 1024 PRO cc_start: 0.8105 (Cg_exo) cc_final: 0.7888 (Cg_endo) REVERT: A 1070 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7752 (mmtm) REVERT: A 1133 LYS cc_start: 0.7371 (tmtt) cc_final: 0.6753 (tptt) REVERT: A 1150 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7750 (mm) REVERT: A 1183 GLN cc_start: 0.7756 (tp40) cc_final: 0.7292 (tp-100) REVERT: A 1221 GLU cc_start: 0.6887 (pt0) cc_final: 0.5613 (tm-30) REVERT: A 1222 LYS cc_start: 0.7334 (tptp) cc_final: 0.6765 (mmtm) REVERT: A 1230 THR cc_start: 0.7827 (p) cc_final: 0.7589 (p) outliers start: 28 outliers final: 17 residues processed: 127 average time/residue: 0.2222 time to fit residues: 40.4392 Evaluate side-chains 122 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 159 VAL 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 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 909 GLN Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1070 LYS 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 1192 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: 20.0000 chunk 89 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.0170 chunk 35 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.197896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139951 restraints weight = 12163.437| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.66 r_work: 0.3494 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10015 Z= 0.137 Angle : 0.518 12.765 13575 Z= 0.257 Chirality : 0.040 0.193 1577 Planarity : 0.003 0.035 1688 Dihedral : 3.581 25.746 1326 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.52 % Allowed : 17.46 % Favored : 80.02 % 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: 1.23 (0.24), residues: 1224 helix: 1.63 (0.18), residues: 814 sheet: 0.40 (0.82), residues: 48 loop : -0.98 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 947 HIS 0.006 0.001 HIS A 153 PHE 0.020 0.001 PHE A 336 TYR 0.012 0.001 TYR A 881 ARG 0.011 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 616) hydrogen bonds : angle 3.75316 ( 1833) covalent geometry : bond 0.00316 (10015) covalent geometry : angle 0.51804 (13575) *********************** 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 135 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.045 Fit side-chains REVERT: A 143 PHE cc_start: 0.7613 (t80) cc_final: 0.6380 (m-10) REVERT: A 173 MET cc_start: 0.9065 (mtp) cc_final: 0.8714 (mtp) REVERT: A 246 ILE cc_start: 0.8309 (tt) cc_final: 0.7999 (mt) REVERT: A 706 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7515 (tpp-160) REVERT: A 744 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7597 (mtp) REVERT: A 909 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7460 (mm-40) REVERT: A 1024 PRO cc_start: 0.8102 (Cg_exo) cc_final: 0.7882 (Cg_endo) REVERT: A 1133 LYS cc_start: 0.7241 (tmtt) cc_final: 0.6586 (tptt) REVERT: A 1150 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7689 (mm) REVERT: A 1183 GLN cc_start: 0.7723 (tp40) cc_final: 0.7216 (tp-100) REVERT: A 1221 GLU cc_start: 0.6947 (pt0) cc_final: 0.5800 (tm-30) REVERT: A 1222 LYS cc_start: 0.7356 (tptp) cc_final: 0.6735 (mmtm) REVERT: A 1230 THR cc_start: 0.7751 (p) cc_final: 0.7520 (p) outliers start: 27 outliers final: 16 residues processed: 128 average time/residue: 0.2494 time to fit residues: 46.6294 Evaluate side-chains 120 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 323 SER 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 909 GLN Chi-restraints excluded: chain A residue 920 GLU 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: 0.6980 chunk 40 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 104 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.0020 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.200429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136205 restraints weight = 12219.497| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.50 r_work: 0.3535 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10015 Z= 0.107 Angle : 0.490 12.532 13575 Z= 0.242 Chirality : 0.038 0.161 1577 Planarity : 0.003 0.036 1688 Dihedral : 3.442 24.886 1326 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.96 % Allowed : 18.39 % Favored : 79.65 % 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: 1.45 (0.25), residues: 1224 helix: 1.81 (0.18), residues: 815 sheet: 0.32 (0.93), residues: 38 loop : -0.89 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.003 0.001 HIS A 153 PHE 0.014 0.001 PHE A 336 TYR 0.010 0.001 TYR A 881 ARG 0.010 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 616) hydrogen bonds : angle 3.63643 ( 1833) covalent geometry : bond 0.00231 (10015) covalent geometry : angle 0.48980 (13575) *********************** 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 128 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 246 ILE cc_start: 0.8434 (tt) cc_final: 0.8084 (mt) REVERT: A 706 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7489 (tpp-160) REVERT: A 909 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7436 (mm-40) REVERT: A 1070 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7493 (mmtm) REVERT: A 1133 LYS cc_start: 0.7236 (tmtt) cc_final: 0.6600 (tptt) REVERT: A 1150 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7616 (mm) REVERT: A 1183 GLN cc_start: 0.7631 (tp40) cc_final: 0.7189 (tp-100) REVERT: A 1221 GLU cc_start: 0.6896 (pt0) cc_final: 0.5736 (tm-30) REVERT: A 1222 LYS cc_start: 0.7298 (tptp) cc_final: 0.6883 (mmtm) outliers start: 21 outliers final: 9 residues processed: 124 average time/residue: 0.2429 time to fit residues: 44.1821 Evaluate side-chains 111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 1070 LYS 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: 0.9980 chunk 50 optimal weight: 8.9990 chunk 113 optimal weight: 0.3980 chunk 1 optimal weight: 0.0010 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 931 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.200171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140047 restraints weight = 12203.434| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.17 r_work: 0.3513 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10015 Z= 0.109 Angle : 0.495 12.802 13575 Z= 0.243 Chirality : 0.039 0.171 1577 Planarity : 0.003 0.036 1688 Dihedral : 3.441 24.584 1326 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.77 % Allowed : 18.58 % Favored : 79.65 % 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: 1.51 (0.25), residues: 1224 helix: 1.83 (0.18), residues: 817 sheet: 0.38 (0.93), residues: 38 loop : -0.81 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.004 0.001 HIS A 153 PHE 0.015 0.001 PHE A 336 TYR 0.010 0.001 TYR A 881 ARG 0.009 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 616) hydrogen bonds : angle 3.62769 ( 1833) covalent geometry : bond 0.00240 (10015) covalent geometry : angle 0.49525 (13575) *********************** 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 121 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 35 HIS cc_start: 0.7953 (t70) cc_final: 0.7593 (t70) REVERT: A 173 MET cc_start: 0.8897 (mtm) cc_final: 0.8686 (mtp) REVERT: A 246 ILE cc_start: 0.8364 (tt) cc_final: 0.7999 (mt) REVERT: A 706 ARG cc_start: 0.7834 (ttt180) cc_final: 0.7450 (tpp-160) REVERT: A 1070 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7461 (mmtm) REVERT: A 1133 LYS cc_start: 0.7179 (tmtt) cc_final: 0.6540 (tptt) REVERT: A 1150 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7349 (mm) REVERT: A 1183 GLN cc_start: 0.7618 (tp40) cc_final: 0.7159 (tp-100) REVERT: A 1221 GLU cc_start: 0.6889 (pt0) cc_final: 0.5724 (tm-30) REVERT: A 1222 LYS cc_start: 0.7371 (tptp) cc_final: 0.6892 (mmtm) outliers start: 19 outliers final: 15 residues processed: 118 average time/residue: 0.2660 time to fit residues: 47.5105 Evaluate side-chains 116 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1070 LYS 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 109 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 96 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.200302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134636 restraints weight = 12183.538| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.55 r_work: 0.3490 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10015 Z= 0.111 Angle : 0.498 13.299 13575 Z= 0.244 Chirality : 0.039 0.155 1577 Planarity : 0.003 0.035 1688 Dihedral : 3.457 23.899 1326 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.06 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: 1.56 (0.25), residues: 1224 helix: 1.85 (0.18), residues: 817 sheet: 0.37 (0.93), residues: 38 loop : -0.73 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 947 HIS 0.004 0.001 HIS A 153 PHE 0.015 0.001 PHE A 336 TYR 0.010 0.001 TYR A 881 ARG 0.009 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 616) hydrogen bonds : angle 3.62181 ( 1833) covalent geometry : bond 0.00242 (10015) covalent geometry : angle 0.49776 (13575) ********************** 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 126 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 246 ILE cc_start: 0.8161 (tt) cc_final: 0.7806 (mt) REVERT: A 262 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.6882 (mmt180) REVERT: A 706 ARG cc_start: 0.7922 (ttt180) cc_final: 0.7402 (tpp-160) REVERT: A 834 ASP cc_start: 0.8283 (m-30) cc_final: 0.8053 (m-30) REVERT: A 1018 ASP cc_start: 0.7212 (m-30) cc_final: 0.6833 (m-30) REVERT: A 1070 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7411 (mmtm) REVERT: A 1133 LYS cc_start: 0.7142 (tmtt) cc_final: 0.6500 (tptt) REVERT: A 1150 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7322 (mm) REVERT: A 1183 GLN cc_start: 0.7554 (tp40) cc_final: 0.7099 (tp-100) REVERT: A 1221 GLU cc_start: 0.7074 (pt0) cc_final: 0.5783 (tm-30) REVERT: A 1222 LYS cc_start: 0.7500 (tptp) cc_final: 0.6962 (mmtm) outliers start: 21 outliers final: 18 residues processed: 123 average time/residue: 0.2006 time to fit residues: 36.1163 Evaluate side-chains 119 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1070 LYS 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 74 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.193013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133914 restraints weight = 12120.751| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.76 r_work: 0.3394 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10015 Z= 0.190 Angle : 0.579 12.331 13575 Z= 0.288 Chirality : 0.042 0.155 1577 Planarity : 0.004 0.041 1688 Dihedral : 3.862 26.938 1326 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.05 % Allowed : 19.14 % Favored : 78.80 % 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: 1.16 (0.24), residues: 1224 helix: 1.51 (0.18), residues: 815 sheet: 0.22 (0.91), residues: 38 loop : -0.78 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 947 HIS 0.008 0.001 HIS A 153 PHE 0.026 0.002 PHE A 352 TYR 0.015 0.001 TYR A 881 ARG 0.009 0.001 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 616) hydrogen bonds : angle 3.91975 ( 1833) covalent geometry : bond 0.00456 (10015) covalent geometry : angle 0.57915 (13575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5936.38 seconds wall clock time: 104 minutes 21.57 seconds (6261.57 seconds total)