Starting phenix.real_space_refine on Mon Jul 28 20:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q5z_13847/07_2025/7q5z_13847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q5z_13847/07_2025/7q5z_13847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q5z_13847/07_2025/7q5z_13847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q5z_13847/07_2025/7q5z_13847.map" model { file = "/net/cci-nas-00/data/ceres_data/7q5z_13847/07_2025/7q5z_13847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q5z_13847/07_2025/7q5z_13847.cif" } resolution = 3.25 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= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6709 2.51 5 N 1719 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10489 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10489 Classifications: {'peptide': 1344} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 70, 'TRANS': 1272} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.71, per 1000 atoms: 0.64 Number of scatterers: 10489 At special positions: 0 Unit cell: (87.2329, 106.004, 141.339, 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 52 16.00 O 2009 8.00 N 1719 7.00 C 6709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1453 " distance=2.03 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: 2.69 Conformation dependent library (CDL) restraints added in 1.6 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 16.1% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 365 through 369 removed outlier: 4.164A pdb=" N ASP A 368 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 602 removed outlier: 4.100A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 973 through 977 removed outlier: 3.755A pdb=" N VAL A 976 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 991 removed outlier: 3.652A pdb=" N ILE A 982 " --> pdb=" O PHE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1014 Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1055 through 1069 removed outlier: 3.900A pdb=" N ILE A1059 " --> pdb=" O ASP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1109 removed outlier: 3.531A pdb=" N GLY A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1125 Processing helix chain 'A' and resid 1133 through 1147 removed outlier: 3.737A pdb=" N ALA A1147 " --> pdb=" O ILE A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1161 removed outlier: 3.997A pdb=" N ILE A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1205 removed outlier: 3.689A pdb=" N GLU A1195 " --> pdb=" O ALA A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1226 removed outlier: 3.602A pdb=" N LYS A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1255 Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.962A pdb=" N ARG A1283 " --> pdb=" O SER A1280 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A1284 " --> pdb=" O VAL A1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1280 through 1284' Processing helix chain 'A' and resid 1380 through 1387 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 5.551A pdb=" N LEU A 31 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 56 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS A 64 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 32 removed outlier: 5.551A pdb=" N LEU A 31 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.487A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 285 removed outlier: 6.517A pdb=" N ALA A 253 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR A 317 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN A 255 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 315 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 257 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN A 313 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N CYS A 259 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN A 311 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS A 261 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.513A pdb=" N VAL A 470 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 499 through 501 Processing sheet with id=AB3, first strand: chain 'A' and resid 499 through 501 removed outlier: 5.792A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB5, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB6, first strand: chain 'A' and resid 741 through 743 Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795 removed outlier: 3.644A pdb=" N THR A 811 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 795 " --> pdb=" O THR A 809 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 809 " --> pdb=" O THR A 795 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 832 through 836 Processing sheet with id=AB9, first strand: chain 'A' and resid 799 through 801 removed outlier: 6.269A pdb=" N VAL A 800 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AC2, first strand: chain 'A' and resid 908 through 913 removed outlier: 3.880A pdb=" N TYR A1309 " --> pdb=" O LEU A 949 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 921 through 930 removed outlier: 4.485A pdb=" N LYS A 923 " --> pdb=" O GLY A1304 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A1304 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1164 through 1167 Processing sheet with id=AC5, first strand: chain 'A' and resid 1327 through 1332 Processing sheet with id=AC6, first strand: chain 'A' and resid 1393 through 1396 removed outlier: 4.014A pdb=" N LYS A1393 " --> pdb=" O TYR A1404 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A1432 " --> pdb=" O LYS A1370 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1134 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: 5.02 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3209 1.34 - 1.46: 2476 1.46 - 1.58: 4958 1.58 - 1.71: 1 1.71 - 1.83: 79 Bond restraints: 10723 Sorted by residual: bond pdb=" CA ASP A1113 " pdb=" C ASP A1113 " ideal model delta sigma weight residual 1.523 1.562 -0.040 1.41e-02 5.03e+03 7.95e+00 bond pdb=" N ASP A 367 " pdb=" CA ASP A 367 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" C SER A1343 " pdb=" N PRO A1344 " ideal model delta sigma weight residual 1.334 1.386 -0.053 2.34e-02 1.83e+03 5.04e+00 bond pdb=" CB PRO A 85 " pdb=" CG PRO A 85 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" CA MET A1378 " pdb=" CB MET A1378 " ideal model delta sigma weight residual 1.513 1.561 -0.048 2.59e-02 1.49e+03 3.38e+00 ... (remaining 10718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 14385 3.64 - 7.28: 143 7.28 - 10.92: 38 10.92 - 14.56: 4 14.56 - 18.20: 1 Bond angle restraints: 14571 Sorted by residual: angle pdb=" N ILE A 760 " pdb=" CA ILE A 760 " pdb=" C ILE A 760 " ideal model delta sigma weight residual 113.47 106.82 6.65 1.01e+00 9.80e-01 4.34e+01 angle pdb=" CB MET A1087 " pdb=" CG MET A1087 " pdb=" SD MET A1087 " ideal model delta sigma weight residual 112.70 130.90 -18.20 3.00e+00 1.11e-01 3.68e+01 angle pdb=" C ALA A1086 " pdb=" N MET A1087 " pdb=" CA MET A1087 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" N GLU A1007 " pdb=" CA GLU A1007 " pdb=" CB GLU A1007 " ideal model delta sigma weight residual 110.40 119.96 -9.56 1.63e+00 3.76e-01 3.44e+01 angle pdb=" CA PRO A 85 " pdb=" N PRO A 85 " pdb=" CD PRO A 85 " ideal model delta sigma weight residual 112.00 104.68 7.32 1.40e+00 5.10e-01 2.73e+01 ... (remaining 14566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5952 17.63 - 35.25: 416 35.25 - 52.88: 68 52.88 - 70.51: 15 70.51 - 88.13: 8 Dihedral angle restraints: 6459 sinusoidal: 2552 harmonic: 3907 Sorted by residual: dihedral pdb=" CA PHE A1235 " pdb=" C PHE A1235 " pdb=" N SER A1236 " pdb=" CA SER A1236 " ideal model delta harmonic sigma weight residual 180.00 -148.90 -31.10 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ALA A1086 " pdb=" C ALA A1086 " pdb=" N MET A1087 " pdb=" CA MET A1087 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LYS A1088 " pdb=" C LYS A1088 " pdb=" N GLY A1089 " pdb=" CA GLY A1089 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 6456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1517 0.109 - 0.217: 133 0.217 - 0.326: 6 0.326 - 0.435: 1 0.435 - 0.544: 2 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CB ILE A 539 " pdb=" CA ILE A 539 " pdb=" CG1 ILE A 539 " pdb=" CG2 ILE A 539 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CB VAL A 594 " pdb=" CA VAL A 594 " pdb=" CG1 VAL A 594 " pdb=" CG2 VAL A 594 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CB ILE A 115 " pdb=" CA ILE A 115 " pdb=" CG1 ILE A 115 " pdb=" CG2 ILE A 115 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 1656 not shown) Planarity restraints: 1870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 84 " -0.102 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO A 85 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1142 " 0.040 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" CG TYR A1142 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 TYR A1142 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1142 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A1142 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A1142 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A1142 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1113 " 0.022 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" CG ASP A1113 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASP A1113 " 0.028 2.00e-02 2.50e+03 pdb=" OD2 ASP A1113 " 0.026 2.00e-02 2.50e+03 ... (remaining 1867 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 9 2.38 - 3.01: 5119 3.01 - 3.64: 15503 3.64 - 4.27: 23295 4.27 - 4.90: 39032 Nonbonded interactions: 82958 Sorted by model distance: nonbonded pdb=" SG CYS A 970 " pdb=" CD GLN A 973 " model vdw 1.750 3.630 nonbonded pdb=" O THR A1038 " pdb=" OG1 THR A1042 " model vdw 2.323 3.040 nonbonded pdb=" OG1 THR A 58 " pdb=" O LYS A 61 " model vdw 2.337 3.040 nonbonded pdb=" OE1 GLU A 972 " pdb=" OH TYR A1439 " model vdw 2.352 3.040 nonbonded pdb=" O PRO A1377 " pdb=" OG1 THR A1381 " model vdw 2.359 3.040 ... (remaining 82953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.410 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: 28.810 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 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 : 0.005 0.100 10734 Z= 0.221 Angle : 1.004 18.201 14593 Z= 0.517 Chirality : 0.062 0.544 1659 Planarity : 0.008 0.151 1870 Dihedral : 12.761 88.132 3916 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.16 % Favored : 93.62 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.07 (0.21), residues: 1332 helix: -2.57 (0.26), residues: 211 sheet: 0.06 (0.23), residues: 526 loop : -2.25 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1224 HIS 0.002 0.001 HIS A1084 PHE 0.028 0.003 PHE A1040 TYR 0.100 0.003 TYR A1142 ARG 0.004 0.001 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.12881 ( 396) hydrogen bonds : angle 6.67765 ( 1134) SS BOND : bond 0.00228 ( 11) SS BOND : angle 1.49900 ( 22) covalent geometry : bond 0.00473 (10723) covalent geometry : angle 1.00318 (14571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 PHE cc_start: 0.8053 (p90) cc_final: 0.7606 (p90) REVERT: A 523 THR cc_start: 0.7805 (p) cc_final: 0.7490 (p) REVERT: A 531 ASP cc_start: 0.8375 (p0) cc_final: 0.7609 (p0) REVERT: A 988 LEU cc_start: 0.8280 (mt) cc_final: 0.7799 (mt) REVERT: A 1060 GLN cc_start: 0.6778 (tm-30) cc_final: 0.6452 (tm-30) outliers start: 1 outliers final: 1 residues processed: 117 average time/residue: 0.1877 time to fit residues: 34.1307 Evaluate side-chains 86 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 973 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.0980 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.147372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.113434 restraints weight = 25626.719| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 4.13 r_work: 0.3900 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10734 Z= 0.127 Angle : 0.617 11.217 14593 Z= 0.313 Chirality : 0.045 0.154 1659 Planarity : 0.005 0.087 1870 Dihedral : 5.034 45.718 1438 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 0.85 % Allowed : 6.22 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 (0.22), residues: 1332 helix: -1.21 (0.31), residues: 213 sheet: 0.13 (0.23), residues: 535 loop : -1.99 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1224 HIS 0.003 0.001 HIS A1229 PHE 0.015 0.001 PHE A 219 TYR 0.025 0.001 TYR A1142 ARG 0.003 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 396) hydrogen bonds : angle 5.45811 ( 1134) SS BOND : bond 0.00143 ( 11) SS BOND : angle 0.88904 ( 22) covalent geometry : bond 0.00293 (10723) covalent geometry : angle 0.61694 (14571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8514 (p0) cc_final: 0.7819 (p0) REVERT: A 1037 LEU cc_start: 0.8373 (tp) cc_final: 0.8005 (tp) REVERT: A 1060 GLN cc_start: 0.6986 (tm-30) cc_final: 0.6534 (tm-30) REVERT: A 1206 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.5087 (m) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.1898 time to fit residues: 29.5046 Evaluate side-chains 92 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN A 857 ASN ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.148677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.113559 restraints weight = 25835.980| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 4.14 r_work: 0.3681 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.163 10734 Z= 0.271 Angle : 0.705 10.249 14593 Z= 0.362 Chirality : 0.048 0.162 1659 Planarity : 0.005 0.068 1870 Dihedral : 5.072 26.506 1435 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 1.53 % Allowed : 9.04 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.46 (0.22), residues: 1332 helix: -1.09 (0.32), residues: 213 sheet: 0.10 (0.23), residues: 514 loop : -1.88 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 739 HIS 0.008 0.001 HIS A1084 PHE 0.021 0.002 PHE A1053 TYR 0.025 0.002 TYR A1436 ARG 0.004 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 396) hydrogen bonds : angle 5.62280 ( 1134) SS BOND : bond 0.00293 ( 11) SS BOND : angle 0.86416 ( 22) covalent geometry : bond 0.00652 (10723) covalent geometry : angle 0.70438 (14571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7430 (mpp) cc_final: 0.7038 (mmt) REVERT: A 250 MET cc_start: 0.6210 (pmm) cc_final: 0.5084 (pmm) REVERT: A 531 ASP cc_start: 0.8674 (p0) cc_final: 0.8226 (p0) REVERT: A 1060 GLN cc_start: 0.7289 (tm-30) cc_final: 0.6846 (tm-30) REVERT: A 1206 THR cc_start: 0.6700 (OUTLIER) cc_final: 0.5603 (m) REVERT: A 1378 MET cc_start: 0.8127 (tmm) cc_final: 0.7880 (tmm) outliers start: 18 outliers final: 12 residues processed: 100 average time/residue: 0.2216 time to fit residues: 35.7823 Evaluate side-chains 95 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 40.0000 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.150881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.116677 restraints weight = 25427.469| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.94 r_work: 0.3804 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10734 Z= 0.149 Angle : 0.597 8.308 14593 Z= 0.306 Chirality : 0.045 0.148 1659 Planarity : 0.004 0.057 1870 Dihedral : 4.778 26.105 1435 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 2.05 % Allowed : 10.83 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 (0.23), residues: 1332 helix: -0.36 (0.35), residues: 212 sheet: 0.18 (0.23), residues: 515 loop : -1.78 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 PHE 0.013 0.001 PHE A1040 TYR 0.015 0.001 TYR A1436 ARG 0.003 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 396) hydrogen bonds : angle 5.31920 ( 1134) SS BOND : bond 0.00164 ( 11) SS BOND : angle 0.79394 ( 22) covalent geometry : bond 0.00358 (10723) covalent geometry : angle 0.59637 (14571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7319 (mpp) cc_final: 0.6985 (mmt) REVERT: A 531 ASP cc_start: 0.8597 (p0) cc_final: 0.8169 (p0) REVERT: A 1037 LEU cc_start: 0.8408 (tp) cc_final: 0.7981 (tp) REVERT: A 1060 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6803 (tm-30) REVERT: A 1206 THR cc_start: 0.6488 (OUTLIER) cc_final: 0.5684 (m) REVERT: A 1378 MET cc_start: 0.8079 (tmm) cc_final: 0.7877 (tmm) REVERT: A 1435 VAL cc_start: 0.7685 (t) cc_final: 0.7379 (p) outliers start: 24 outliers final: 15 residues processed: 104 average time/residue: 0.2634 time to fit residues: 44.7199 Evaluate side-chains 101 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 83 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.151139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.116987 restraints weight = 25537.974| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 4.15 r_work: 0.3820 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10734 Z= 0.145 Angle : 0.609 12.772 14593 Z= 0.305 Chirality : 0.045 0.163 1659 Planarity : 0.004 0.052 1870 Dihedral : 4.677 25.631 1435 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 2.47 % Allowed : 11.59 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.03 (0.23), residues: 1332 helix: -0.09 (0.35), residues: 212 sheet: 0.19 (0.23), residues: 515 loop : -1.68 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 PHE 0.012 0.001 PHE A1040 TYR 0.039 0.001 TYR A1142 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 396) hydrogen bonds : angle 5.15701 ( 1134) SS BOND : bond 0.00151 ( 11) SS BOND : angle 0.73758 ( 22) covalent geometry : bond 0.00347 (10723) covalent geometry : angle 0.60847 (14571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8482 (m-40) cc_final: 0.8083 (m-40) REVERT: A 192 MET cc_start: 0.7360 (mpp) cc_final: 0.7064 (mmt) REVERT: A 531 ASP cc_start: 0.8557 (p0) cc_final: 0.8123 (p0) REVERT: A 953 MET cc_start: 0.7757 (mmm) cc_final: 0.7344 (mmp) REVERT: A 1037 LEU cc_start: 0.8420 (tp) cc_final: 0.8006 (tp) REVERT: A 1060 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6729 (tm-30) REVERT: A 1206 THR cc_start: 0.6241 (OUTLIER) cc_final: 0.5725 (m) REVERT: A 1435 VAL cc_start: 0.7699 (t) cc_final: 0.7400 (p) outliers start: 29 outliers final: 19 residues processed: 102 average time/residue: 0.1689 time to fit residues: 27.9153 Evaluate side-chains 103 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 97 optimal weight: 0.3980 chunk 71 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.152050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.117919 restraints weight = 25836.095| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 4.23 r_work: 0.3824 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10734 Z= 0.123 Angle : 0.603 10.886 14593 Z= 0.302 Chirality : 0.044 0.155 1659 Planarity : 0.004 0.051 1870 Dihedral : 4.545 25.058 1435 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 2.47 % Allowed : 12.28 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 (0.23), residues: 1332 helix: -0.00 (0.35), residues: 214 sheet: 0.25 (0.23), residues: 515 loop : -1.60 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 837 HIS 0.003 0.000 HIS A1084 PHE 0.011 0.001 PHE A1040 TYR 0.019 0.001 TYR A1142 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 396) hydrogen bonds : angle 5.02233 ( 1134) SS BOND : bond 0.00144 ( 11) SS BOND : angle 0.91508 ( 22) covalent geometry : bond 0.00293 (10723) covalent geometry : angle 0.60229 (14571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8404 (m-40) cc_final: 0.8016 (m-40) REVERT: A 531 ASP cc_start: 0.8604 (p0) cc_final: 0.8176 (p0) REVERT: A 1037 LEU cc_start: 0.8350 (tp) cc_final: 0.7595 (tp) REVERT: A 1060 GLN cc_start: 0.7125 (tm-30) cc_final: 0.6689 (tm-30) REVERT: A 1087 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.5043 (pmm) REVERT: A 1206 THR cc_start: 0.6502 (OUTLIER) cc_final: 0.5458 (m) REVERT: A 1324 MET cc_start: 0.7030 (mmt) cc_final: 0.6578 (mmp) REVERT: A 1435 VAL cc_start: 0.7664 (t) cc_final: 0.7378 (p) outliers start: 29 outliers final: 21 residues processed: 106 average time/residue: 0.1707 time to fit residues: 29.1903 Evaluate side-chains 108 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.151211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.117247 restraints weight = 25968.671| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.95 r_work: 0.3827 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10734 Z= 0.146 Angle : 0.605 11.157 14593 Z= 0.303 Chirality : 0.044 0.154 1659 Planarity : 0.004 0.049 1870 Dihedral : 4.522 25.235 1435 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 2.81 % Allowed : 12.45 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.90 (0.23), residues: 1332 helix: -0.00 (0.35), residues: 214 sheet: 0.21 (0.23), residues: 521 loop : -1.54 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 PHE 0.011 0.001 PHE A 618 TYR 0.046 0.001 TYR A1142 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 396) hydrogen bonds : angle 5.00434 ( 1134) SS BOND : bond 0.00173 ( 11) SS BOND : angle 0.84525 ( 22) covalent geometry : bond 0.00352 (10723) covalent geometry : angle 0.60434 (14571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8369 (m-40) cc_final: 0.7986 (m-40) REVERT: A 342 MET cc_start: 0.1933 (mmm) cc_final: 0.1636 (mmm) REVERT: A 531 ASP cc_start: 0.8590 (p0) cc_final: 0.8157 (p0) REVERT: A 953 MET cc_start: 0.7592 (mmm) cc_final: 0.7207 (mmp) REVERT: A 1060 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6726 (tm-30) REVERT: A 1087 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.5055 (pmm) REVERT: A 1142 TYR cc_start: 0.5885 (t80) cc_final: 0.5523 (t80) REVERT: A 1206 THR cc_start: 0.6156 (OUTLIER) cc_final: 0.5589 (m) REVERT: A 1435 VAL cc_start: 0.7659 (t) cc_final: 0.7361 (p) outliers start: 33 outliers final: 26 residues processed: 105 average time/residue: 0.1755 time to fit residues: 29.6846 Evaluate side-chains 114 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 126 optimal weight: 0.0170 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1293 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 = 0.4455 r_free = 0.4455 target = 0.148689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.113895 restraints weight = 25905.357| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.22 r_work: 0.3772 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 10734 Z= 0.221 Angle : 0.669 11.933 14593 Z= 0.338 Chirality : 0.046 0.166 1659 Planarity : 0.004 0.048 1870 Dihedral : 4.796 26.422 1435 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.17 % Rotamer: Outliers : 3.15 % Allowed : 12.79 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 (0.23), residues: 1332 helix: -0.45 (0.33), residues: 216 sheet: 0.18 (0.23), residues: 519 loop : -1.64 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 837 HIS 0.006 0.001 HIS A 914 PHE 0.015 0.002 PHE A1053 TYR 0.054 0.002 TYR A1142 ARG 0.002 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 396) hydrogen bonds : angle 5.24221 ( 1134) SS BOND : bond 0.00297 ( 11) SS BOND : angle 0.83458 ( 22) covalent geometry : bond 0.00533 (10723) covalent geometry : angle 0.66921 (14571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7910 (mt) cc_final: 0.7650 (mt) REVERT: A 457 ARG cc_start: 0.7555 (ptp-170) cc_final: 0.7326 (ptp-170) REVERT: A 531 ASP cc_start: 0.8637 (p0) cc_final: 0.8197 (p0) REVERT: A 1037 LEU cc_start: 0.8249 (tp) cc_final: 0.7778 (tp) REVERT: A 1087 MET cc_start: 0.5681 (OUTLIER) cc_final: 0.5234 (pmm) REVERT: A 1206 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.5867 (m) REVERT: A 1435 VAL cc_start: 0.7866 (t) cc_final: 0.7557 (p) outliers start: 37 outliers final: 31 residues processed: 113 average time/residue: 0.1733 time to fit residues: 30.7688 Evaluate side-chains 115 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 89 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.0010 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.150746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.116689 restraints weight = 26012.872| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 4.02 r_work: 0.3816 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10734 Z= 0.136 Angle : 0.623 10.936 14593 Z= 0.313 Chirality : 0.045 0.223 1659 Planarity : 0.004 0.048 1870 Dihedral : 4.614 25.808 1435 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 2.81 % Allowed : 13.55 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 (0.23), residues: 1332 helix: -0.04 (0.35), residues: 214 sheet: 0.24 (0.23), residues: 515 loop : -1.57 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 837 HIS 0.003 0.001 HIS A1084 PHE 0.012 0.001 PHE A1040 TYR 0.076 0.001 TYR A1142 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 396) hydrogen bonds : angle 5.09420 ( 1134) SS BOND : bond 0.00212 ( 11) SS BOND : angle 0.82641 ( 22) covalent geometry : bond 0.00328 (10723) covalent geometry : angle 0.62256 (14571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 99 SER cc_start: 0.7957 (p) cc_final: 0.7659 (m) REVERT: A 192 MET cc_start: 0.7077 (mmt) cc_final: 0.6749 (mpp) REVERT: A 531 ASP cc_start: 0.8574 (p0) cc_final: 0.8123 (p0) REVERT: A 953 MET cc_start: 0.7585 (mmm) cc_final: 0.7086 (mmp) REVERT: A 1037 LEU cc_start: 0.8034 (tp) cc_final: 0.7688 (tp) REVERT: A 1087 MET cc_start: 0.5578 (OUTLIER) cc_final: 0.5175 (pmm) REVERT: A 1206 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.5585 (m) REVERT: A 1435 VAL cc_start: 0.7688 (t) cc_final: 0.7398 (p) outliers start: 33 outliers final: 27 residues processed: 107 average time/residue: 0.1661 time to fit residues: 28.8334 Evaluate side-chains 117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.0020 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 69 optimal weight: 0.0770 chunk 4 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.152627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.118770 restraints weight = 25728.252| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 4.42 r_work: 0.3849 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10734 Z= 0.113 Angle : 0.624 10.833 14593 Z= 0.313 Chirality : 0.045 0.218 1659 Planarity : 0.004 0.049 1870 Dihedral : 4.473 25.111 1435 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.22 % Allowed : 14.24 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.77 (0.24), residues: 1332 helix: 0.14 (0.36), residues: 214 sheet: 0.35 (0.24), residues: 512 loop : -1.50 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 837 HIS 0.002 0.000 HIS A1084 PHE 0.013 0.001 PHE A1040 TYR 0.063 0.001 TYR A1142 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 396) hydrogen bonds : angle 4.99193 ( 1134) SS BOND : bond 0.00170 ( 11) SS BOND : angle 0.76861 ( 22) covalent geometry : bond 0.00267 (10723) covalent geometry : angle 0.62363 (14571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8331 (m-40) cc_final: 0.7891 (m-40) REVERT: A 99 SER cc_start: 0.8138 (p) cc_final: 0.7892 (m) REVERT: A 531 ASP cc_start: 0.8547 (p0) cc_final: 0.8095 (p0) REVERT: A 953 MET cc_start: 0.7575 (mmm) cc_final: 0.6973 (mmp) REVERT: A 1087 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5402 (pmm) REVERT: A 1206 THR cc_start: 0.6029 (OUTLIER) cc_final: 0.5550 (m) REVERT: A 1435 VAL cc_start: 0.7642 (t) cc_final: 0.7382 (p) outliers start: 26 outliers final: 21 residues processed: 106 average time/residue: 0.1726 time to fit residues: 29.5505 Evaluate side-chains 113 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 49 optimal weight: 0.0040 chunk 132 optimal weight: 0.5980 chunk 27 optimal weight: 0.0000 chunk 85 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A1293 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 = 0.4516 r_free = 0.4516 target = 0.152965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.119340 restraints weight = 25686.101| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.26 r_work: 0.3858 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10734 Z= 0.119 Angle : 0.627 15.247 14593 Z= 0.311 Chirality : 0.044 0.232 1659 Planarity : 0.004 0.048 1870 Dihedral : 4.365 24.653 1435 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 2.39 % Allowed : 14.24 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.78 (0.23), residues: 1332 helix: -0.03 (0.35), residues: 213 sheet: 0.39 (0.24), residues: 512 loop : -1.51 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 837 HIS 0.002 0.000 HIS A1084 PHE 0.016 0.001 PHE A1144 TYR 0.048 0.001 TYR A1142 ARG 0.002 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 396) hydrogen bonds : angle 4.92336 ( 1134) SS BOND : bond 0.00199 ( 11) SS BOND : angle 0.78248 ( 22) covalent geometry : bond 0.00280 (10723) covalent geometry : angle 0.62693 (14571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6889.09 seconds wall clock time: 123 minutes 32.01 seconds (7412.01 seconds total)