Starting phenix.real_space_refine on Fri Feb 14 21:45:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q5z_13847/02_2025/7q5z_13847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q5z_13847/02_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_13847/02_2025/7q5z_13847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q5z_13847/02_2025/7q5z_13847.map" model { file = "/net/cci-nas-00/data/ceres_data/7q5z_13847/02_2025/7q5z_13847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q5z_13847/02_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-5592/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: 6.53, per 1000 atoms: 0.62 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: 2.23 Conformation dependent library (CDL) restraints added in 1.3 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: 4.78 Time building geometry restraints manager: 2.67 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: 1.380 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: 0.110 Process input model: 27.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- 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 10723 Z= 0.307 Angle : 1.003 18.201 14571 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 *********************** 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 : 1.190 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: 0.1953 time to fit residues: 35.1571 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 : 1.165 ------------------------------------------------------------------------------- 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: 0.0040 chunk 121 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.156474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.123114 restraints weight = 25464.883| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 4.31 r_work: 0.3921 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10723 Z= 0.165 Angle : 0.606 11.507 14571 Z= 0.307 Chirality : 0.044 0.157 1659 Planarity : 0.005 0.085 1870 Dihedral : 5.013 45.972 1438 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 0.68 % Allowed : 6.48 % Favored : 92.84 % 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: -1.49 (0.22), residues: 1332 helix: -1.16 (0.31), residues: 213 sheet: 0.16 (0.23), residues: 532 loop : -2.02 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1224 HIS 0.002 0.001 HIS A1018 PHE 0.017 0.001 PHE A 219 TYR 0.023 0.001 TYR A1142 ARG 0.003 0.000 ARG A 605 *********************** 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: 8 poor density : 99 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 192 MET cc_start: 0.7223 (mpp) cc_final: 0.6777 (mmp) REVERT: A 518 PHE cc_start: 0.8370 (p90) cc_final: 0.8144 (p90) REVERT: A 531 ASP cc_start: 0.8488 (p0) cc_final: 0.7789 (p0) REVERT: A 1037 LEU cc_start: 0.8346 (tp) cc_final: 0.7980 (tp) REVERT: A 1060 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6507 (tm-30) outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 0.1977 time to fit residues: 30.8347 Evaluate side-chains 87 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 1367 VAL 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: 4.9990 chunk 24 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 854 HIS ** 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 = 0.4482 r_free = 0.4482 target = 0.150652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.115809 restraints weight = 25829.732| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 4.24 r_work: 0.3795 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 10723 Z= 0.316 Angle : 0.651 9.761 14571 Z= 0.333 Chirality : 0.047 0.159 1659 Planarity : 0.005 0.096 1870 Dihedral : 4.859 25.715 1435 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 1.62 % Allowed : 8.44 % Favored : 89.94 % 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: -1.31 (0.23), residues: 1332 helix: -0.83 (0.32), residues: 212 sheet: 0.20 (0.23), residues: 518 loop : -1.86 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 837 HIS 0.006 0.001 HIS A1084 PHE 0.020 0.002 PHE A1053 TYR 0.021 0.002 TYR A1436 ARG 0.007 0.000 ARG A 97 *********************** 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 111 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7407 (mpp) cc_final: 0.7031 (mmt) REVERT: A 250 MET cc_start: 0.6331 (pmm) cc_final: 0.5128 (pmm) REVERT: A 531 ASP cc_start: 0.8631 (p0) cc_final: 0.8203 (p0) REVERT: A 766 MET cc_start: 0.5909 (ttm) cc_final: 0.5458 (tmm) REVERT: A 1060 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6723 (tm-30) REVERT: A 1206 THR cc_start: 0.6900 (OUTLIER) cc_final: 0.5842 (m) REVERT: A 1378 MET cc_start: 0.8119 (tmm) cc_final: 0.7843 (tmm) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.2037 time to fit residues: 32.7635 Evaluate side-chains 97 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 204 LYS 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: 0.7980 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 40.0000 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 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** A1229 HIS ** 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 = 0.4498 r_free = 0.4498 target = 0.151912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.117425 restraints weight = 25510.560| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 4.40 r_work: 0.3826 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10723 Z= 0.218 Angle : 0.597 12.506 14571 Z= 0.303 Chirality : 0.044 0.170 1659 Planarity : 0.004 0.055 1870 Dihedral : 4.673 25.248 1435 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 1.53 % Allowed : 11.17 % Favored : 87.30 % 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: -1.08 (0.23), residues: 1332 helix: -0.24 (0.35), residues: 212 sheet: 0.26 (0.23), residues: 519 loop : -1.78 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 PHE 0.019 0.001 PHE A 219 TYR 0.030 0.001 TYR A1142 ARG 0.003 0.000 ARG A 97 *********************** 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 107 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7306 (mpp) cc_final: 0.6908 (mmt) REVERT: A 531 ASP cc_start: 0.8589 (p0) cc_final: 0.8160 (p0) REVERT: A 1037 LEU cc_start: 0.8397 (tp) cc_final: 0.7982 (tp) REVERT: A 1060 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6743 (tm-30) REVERT: A 1206 THR cc_start: 0.6646 (OUTLIER) cc_final: 0.5756 (m) REVERT: A 1378 MET cc_start: 0.8100 (tmm) cc_final: 0.7894 (tmm) REVERT: A 1435 VAL cc_start: 0.7593 (t) cc_final: 0.7278 (p) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 0.1854 time to fit residues: 29.1146 Evaluate side-chains 94 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 130 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 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: 4.9990 chunk 132 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.152740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.118430 restraints weight = 25535.852| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 4.33 r_work: 0.3846 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10723 Z= 0.182 Angle : 0.584 11.418 14571 Z= 0.292 Chirality : 0.044 0.149 1659 Planarity : 0.004 0.051 1870 Dihedral : 4.521 24.946 1435 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 1.88 % Allowed : 11.42 % Favored : 86.70 % 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: -0.88 (0.23), residues: 1332 helix: 0.09 (0.35), residues: 212 sheet: 0.33 (0.24), residues: 514 loop : -1.66 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 837 HIS 0.003 0.001 HIS A1084 PHE 0.019 0.001 PHE A 219 TYR 0.029 0.001 TYR A1142 ARG 0.002 0.000 ARG A 97 *********************** 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 111 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8427 (m-40) cc_final: 0.8044 (m-40) REVERT: A 501 MET cc_start: 0.8371 (mpp) cc_final: 0.8157 (mpp) REVERT: A 531 ASP cc_start: 0.8520 (p0) cc_final: 0.8065 (p0) REVERT: A 766 MET cc_start: 0.6125 (ttm) cc_final: 0.5467 (tmm) REVERT: A 953 MET cc_start: 0.7737 (mmm) cc_final: 0.7292 (mmp) REVERT: A 1037 LEU cc_start: 0.8333 (tp) cc_final: 0.7865 (tp) REVERT: A 1060 GLN cc_start: 0.7033 (tm-30) cc_final: 0.6566 (tm-30) REVERT: A 1116 MET cc_start: 0.7412 (mmp) cc_final: 0.7161 (mmp) REVERT: A 1206 THR cc_start: 0.6592 (OUTLIER) cc_final: 0.5362 (m) REVERT: A 1435 VAL cc_start: 0.7670 (t) cc_final: 0.7395 (p) outliers start: 22 outliers final: 13 residues processed: 103 average time/residue: 0.1759 time to fit residues: 29.0839 Evaluate side-chains 98 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 130 LEU 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 946 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1123 CYS 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: 0.9980 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.153294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.119338 restraints weight = 25868.132| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 4.32 r_work: 0.3859 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10723 Z= 0.174 Angle : 0.587 11.653 14571 Z= 0.293 Chirality : 0.043 0.163 1659 Planarity : 0.004 0.050 1870 Dihedral : 4.420 24.492 1435 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 1.79 % Allowed : 12.45 % Favored : 85.76 % 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: -0.81 (0.23), residues: 1332 helix: 0.17 (0.36), residues: 213 sheet: 0.35 (0.23), residues: 519 loop : -1.62 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 837 HIS 0.003 0.000 HIS A1084 PHE 0.020 0.001 PHE A 219 TYR 0.012 0.001 TYR A1142 ARG 0.001 0.000 ARG A 140 *********************** 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 108 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8404 (m-40) cc_final: 0.8081 (m-40) REVERT: A 531 ASP cc_start: 0.8548 (p0) cc_final: 0.8110 (p0) REVERT: A 766 MET cc_start: 0.6056 (ttm) cc_final: 0.5556 (tmm) REVERT: A 826 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7534 (mm) REVERT: A 1037 LEU cc_start: 0.8328 (tp) cc_final: 0.7881 (tp) REVERT: A 1060 GLN cc_start: 0.7007 (tm-30) cc_final: 0.6550 (tm-30) REVERT: A 1206 THR cc_start: 0.6484 (OUTLIER) cc_final: 0.5535 (m) REVERT: A 1435 VAL cc_start: 0.7638 (t) cc_final: 0.7373 (p) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 0.1796 time to fit residues: 28.9772 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 : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 LEU 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 826 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1206 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: 0.9980 chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 63 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: ** 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 = 0.4512 r_free = 0.4512 target = 0.152864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.118815 restraints weight = 25795.898| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 4.33 r_work: 0.3848 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10723 Z= 0.187 Angle : 0.576 9.204 14571 Z= 0.289 Chirality : 0.043 0.158 1659 Planarity : 0.004 0.047 1870 Dihedral : 4.364 24.503 1435 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 2.47 % Allowed : 12.19 % Favored : 85.34 % 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: -0.76 (0.23), residues: 1332 helix: 0.19 (0.36), residues: 213 sheet: 0.33 (0.23), residues: 525 loop : -1.53 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 837 HIS 0.003 0.000 HIS A1084 PHE 0.018 0.001 PHE A 219 TYR 0.039 0.001 TYR A1142 ARG 0.001 0.000 ARG A 140 *********************** 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 121 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8387 (m-40) cc_final: 0.8086 (m-40) REVERT: A 531 ASP cc_start: 0.8576 (p0) cc_final: 0.8140 (p0) REVERT: A 826 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7557 (mm) REVERT: A 953 MET cc_start: 0.7592 (mmm) cc_final: 0.7253 (mmp) REVERT: A 1037 LEU cc_start: 0.8368 (tp) cc_final: 0.7925 (tp) REVERT: A 1060 GLN cc_start: 0.6996 (tm-30) cc_final: 0.6521 (tm-30) REVERT: A 1206 THR cc_start: 0.6501 (OUTLIER) cc_final: 0.5694 (m) REVERT: A 1435 VAL cc_start: 0.7616 (t) cc_final: 0.7319 (p) outliers start: 29 outliers final: 21 residues processed: 109 average time/residue: 0.1761 time to fit residues: 31.2849 Evaluate side-chains 109 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 LEU 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 523 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 872 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 1123 CYS 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: 2.9990 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.151333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117061 restraints weight = 25791.579| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 4.04 r_work: 0.3813 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10723 Z= 0.250 Angle : 0.627 17.369 14571 Z= 0.313 Chirality : 0.044 0.207 1659 Planarity : 0.004 0.046 1870 Dihedral : 4.438 25.018 1435 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 2.81 % Allowed : 12.36 % Favored : 84.83 % 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: -0.81 (0.23), residues: 1332 helix: 0.03 (0.35), residues: 213 sheet: 0.29 (0.23), residues: 525 loop : -1.52 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 PHE 0.020 0.002 PHE A 219 TYR 0.015 0.001 TYR A1436 ARG 0.001 0.000 ARG A 592 *********************** 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 123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8407 (m-40) cc_final: 0.8076 (m-40) REVERT: A 531 ASP cc_start: 0.8589 (p0) cc_final: 0.8158 (p0) REVERT: A 1037 LEU cc_start: 0.8471 (tp) cc_final: 0.8097 (tp) REVERT: A 1060 GLN cc_start: 0.7088 (tm-30) cc_final: 0.6607 (tm-30) REVERT: A 1206 THR cc_start: 0.6318 (OUTLIER) cc_final: 0.5729 (m) REVERT: A 1324 MET cc_start: 0.7057 (mmt) cc_final: 0.6715 (mmp) REVERT: A 1435 VAL cc_start: 0.7657 (t) cc_final: 0.7339 (p) outliers start: 33 outliers final: 26 residues processed: 109 average time/residue: 0.1746 time to fit residues: 30.3538 Evaluate side-chains 114 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 528 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 872 THR 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 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: 2.9990 chunk 121 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 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 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 = 0.4500 r_free = 0.4500 target = 0.151821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.117568 restraints weight = 25992.836| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 4.13 r_work: 0.3825 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10723 Z= 0.213 Angle : 0.620 16.159 14571 Z= 0.307 Chirality : 0.044 0.166 1659 Planarity : 0.004 0.046 1870 Dihedral : 4.421 25.084 1435 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 2.56 % Allowed : 12.53 % Favored : 84.91 % 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: -0.75 (0.24), residues: 1332 helix: 0.15 (0.35), residues: 213 sheet: 0.35 (0.24), residues: 516 loop : -1.49 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 837 HIS 0.004 0.001 HIS A1084 PHE 0.021 0.001 PHE A 219 TYR 0.013 0.001 TYR A1142 ARG 0.002 0.000 ARG A 140 *********************** 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 118 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8399 (m-40) cc_final: 0.8064 (m-40) REVERT: A 531 ASP cc_start: 0.8550 (p0) cc_final: 0.8099 (p0) REVERT: A 953 MET cc_start: 0.7574 (mmm) cc_final: 0.7090 (mmp) REVERT: A 1060 GLN cc_start: 0.7130 (tm-30) cc_final: 0.6697 (tm-30) REVERT: A 1206 THR cc_start: 0.6471 (OUTLIER) cc_final: 0.5339 (m) REVERT: A 1324 MET cc_start: 0.7078 (mmt) cc_final: 0.6783 (mmp) outliers start: 30 outliers final: 26 residues processed: 105 average time/residue: 0.1709 time to fit residues: 29.0812 Evaluate side-chains 114 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 523 THR Chi-restraints excluded: chain A residue 528 LEU 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 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1123 CYS 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: 0.8980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 97 optimal weight: 0.0070 chunk 119 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 = 0.4515 r_free = 0.4515 target = 0.153009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.118829 restraints weight = 25771.541| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 4.35 r_work: 0.3856 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10723 Z= 0.184 Angle : 0.615 15.997 14571 Z= 0.304 Chirality : 0.044 0.202 1659 Planarity : 0.004 0.046 1870 Dihedral : 4.328 24.609 1435 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.13 % Allowed : 13.21 % Favored : 84.65 % 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: -0.60 (0.24), residues: 1332 helix: 0.36 (0.36), residues: 213 sheet: 0.47 (0.24), residues: 508 loop : -1.44 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 837 HIS 0.002 0.000 HIS A1084 PHE 0.020 0.001 PHE A 219 TYR 0.017 0.001 TYR A1142 ARG 0.002 0.000 ARG A 140 ********************** 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 112 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8354 (m-40) cc_final: 0.8022 (m-40) REVERT: A 531 ASP cc_start: 0.8538 (p0) cc_final: 0.8083 (p0) REVERT: A 953 MET cc_start: 0.7584 (mmm) cc_final: 0.7092 (mmp) REVERT: A 1037 LEU cc_start: 0.7988 (tp) cc_final: 0.7428 (tp) REVERT: A 1060 GLN cc_start: 0.7098 (tm-30) cc_final: 0.6671 (tm-30) REVERT: A 1066 MET cc_start: 0.5050 (mmt) cc_final: 0.4407 (mmt) REVERT: A 1206 THR cc_start: 0.6401 (OUTLIER) cc_final: 0.5601 (m) outliers start: 25 outliers final: 20 residues processed: 101 average time/residue: 0.1744 time to fit residues: 28.6749 Evaluate side-chains 108 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 LEU 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 523 THR Chi-restraints excluded: chain A residue 528 LEU 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 1007 GLU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1123 CYS 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 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 58 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 855 HIS ** 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 = 0.4462 r_free = 0.4462 target = 0.149139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.114292 restraints weight = 25573.943| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 4.17 r_work: 0.3774 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 10723 Z= 0.354 Angle : 0.693 16.453 14571 Z= 0.347 Chirality : 0.047 0.266 1659 Planarity : 0.004 0.045 1870 Dihedral : 4.676 25.745 1435 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.94 % Rotamer: Outliers : 2.47 % Allowed : 12.96 % Favored : 84.57 % 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: -0.92 (0.23), residues: 1332 helix: -0.35 (0.33), residues: 215 sheet: 0.32 (0.24), residues: 518 loop : -1.54 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 837 HIS 0.007 0.001 HIS A1084 PHE 0.020 0.002 PHE A 219 TYR 0.021 0.002 TYR A1142 ARG 0.002 0.000 ARG A 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6483.46 seconds wall clock time: 115 minutes 44.78 seconds (6944.78 seconds total)