Starting phenix.real_space_refine on Tue Mar 11 22:42:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5d_42982/03_2025/8v5d_42982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5d_42982/03_2025/8v5d_42982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v5d_42982/03_2025/8v5d_42982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5d_42982/03_2025/8v5d_42982.map" model { file = "/net/cci-nas-00/data/ceres_data/8v5d_42982/03_2025/8v5d_42982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5d_42982/03_2025/8v5d_42982.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4263 2.51 5 N 1173 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6694 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6694 Classifications: {'peptide': 851} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 793} Chain breaks: 6 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.32, per 1000 atoms: 0.65 Number of scatterers: 6694 At special positions: 0 Unit cell: (79.968, 94.129, 99.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1215 8.00 N 1173 7.00 C 4263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 901.6 milliseconds 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 46.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.731A pdb=" N LEU A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.553A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.986A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.583A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 4.454A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 470 removed outlier: 3.653A pdb=" N ALA A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.510A pdb=" N LYS A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 removed outlier: 3.569A pdb=" N GLU A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 776 " --> pdb=" O PRO A 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 776' Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.582A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 804 " --> pdb=" O PHE A 800 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.527A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 4.245A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 915 through 923 Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 956 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 989 removed outlier: 3.679A pdb=" N GLU A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 989 " --> pdb=" O MET A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1066 removed outlier: 3.783A pdb=" N PHE A1058 " --> pdb=" O GLU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.504A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1169 removed outlier: 3.670A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1211 Processing helix chain 'A' and resid 1219 through 1228 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.651A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A 224 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.196A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA5, first strand: chain 'A' and resid 612 through 615 Processing sheet with id=AA6, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 7.664A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 831 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: 1.83 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2216 1.34 - 1.46: 1501 1.46 - 1.58: 3083 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 6871 Sorted by residual: bond pdb=" CA VAL A 878 " pdb=" CB VAL A 878 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.21e+00 bond pdb=" N PRO A 246 " pdb=" CA PRO A 246 " ideal model delta sigma weight residual 1.469 1.482 -0.014 1.28e-02 6.10e+03 1.14e+00 bond pdb=" CA THR A 914 " pdb=" C THR A 914 " ideal model delta sigma weight residual 1.522 1.508 0.014 1.37e-02 5.33e+03 1.06e+00 bond pdb=" CA ALA A 604 " pdb=" C ALA A 604 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.28e-01 bond pdb=" N PRO A 163 " pdb=" CA PRO A 163 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.70e-01 ... (remaining 6866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 8878 1.01 - 2.03: 346 2.03 - 3.04: 87 3.04 - 4.06: 18 4.06 - 5.07: 10 Bond angle restraints: 9339 Sorted by residual: angle pdb=" CA GLY A1205 " pdb=" C GLY A1205 " pdb=" O GLY A1205 " ideal model delta sigma weight residual 122.37 120.22 2.15 7.30e-01 1.88e+00 8.67e+00 angle pdb=" CA GLY A1205 " pdb=" C GLY A1205 " pdb=" N MET A1206 " ideal model delta sigma weight residual 114.13 116.99 -2.86 1.11e+00 8.12e-01 6.62e+00 angle pdb=" O THR A 914 " pdb=" C THR A 914 " pdb=" N ALA A 915 " ideal model delta sigma weight residual 122.43 125.76 -3.33 1.46e+00 4.69e-01 5.20e+00 angle pdb=" CA THR A 914 " pdb=" C THR A 914 " pdb=" N ALA A 915 " ideal model delta sigma weight residual 118.41 115.43 2.98 1.34e+00 5.57e-01 4.93e+00 angle pdb=" C ILE A 245 " pdb=" N PRO A 246 " pdb=" CA PRO A 246 " ideal model delta sigma weight residual 119.84 122.59 -2.75 1.25e+00 6.40e-01 4.82e+00 ... (remaining 9334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 3875 16.24 - 32.48: 182 32.48 - 48.73: 35 48.73 - 64.97: 3 64.97 - 81.21: 2 Dihedral angle restraints: 4097 sinusoidal: 1648 harmonic: 2449 Sorted by residual: dihedral pdb=" CA SER A 810 " pdb=" C SER A 810 " pdb=" N GLN A 811 " pdb=" CA GLN A 811 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ARG A 869 " pdb=" CB ARG A 869 " pdb=" CG ARG A 869 " pdb=" CD ARG A 869 " ideal model delta sinusoidal sigma weight residual -180.00 -122.19 -57.81 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N PHE A1164 " pdb=" CA PHE A1164 " pdb=" CB PHE A1164 " pdb=" CG PHE A1164 " ideal model delta sinusoidal sigma weight residual -180.00 -128.38 -51.62 3 1.50e+01 4.44e-03 9.03e+00 ... (remaining 4094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 602 0.028 - 0.055: 258 0.055 - 0.083: 79 0.083 - 0.110: 53 0.110 - 0.138: 12 Chirality restraints: 1004 Sorted by residual: chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL A 845 " pdb=" N VAL A 845 " pdb=" C VAL A 845 " pdb=" CB VAL A 845 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1001 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 73 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 588 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 589 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 240 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO A 241 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.021 5.00e-02 4.00e+02 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 990 2.75 - 3.29: 6349 3.29 - 3.83: 11352 3.83 - 4.36: 12933 4.36 - 4.90: 22597 Nonbonded interactions: 54221 Sorted by model distance: nonbonded pdb=" O LYS A 990 " pdb=" OG SER A1055 " model vdw 2.219 3.040 nonbonded pdb=" O MET A 797 " pdb=" N VAL A 870 " model vdw 2.225 3.120 nonbonded pdb=" NH2 ARG A 417 " pdb=" O ILE A1079 " model vdw 2.227 3.120 nonbonded pdb=" O ASN A 795 " pdb=" OG SER A 799 " model vdw 2.245 3.040 nonbonded pdb=" O ALA A 957 " pdb=" OH TYR A 986 " model vdw 2.246 3.040 ... (remaining 54216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.590 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.470 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 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 : 0.003 0.035 6871 Z= 0.188 Angle : 0.519 5.071 9339 Z= 0.280 Chirality : 0.039 0.138 1004 Planarity : 0.004 0.050 1214 Dihedral : 9.897 81.209 2519 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.84 % Allowed : 4.26 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.80 (0.29), residues: 837 helix: 1.52 (0.28), residues: 345 sheet: 0.76 (0.61), residues: 82 loop : -0.33 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 859 HIS 0.005 0.001 HIS A 971 PHE 0.010 0.001 PHE A 389 TYR 0.010 0.001 TYR A1166 ARG 0.003 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 TYR cc_start: 0.6369 (t80) cc_final: 0.5555 (t80) REVERT: A 452 TYR cc_start: 0.7765 (t80) cc_final: 0.6909 (t80) REVERT: A 907 PHE cc_start: 0.6614 (t80) cc_final: 0.6252 (t80) REVERT: A 986 TYR cc_start: 0.7064 (m-80) cc_final: 0.6436 (m-80) outliers start: 13 outliers final: 4 residues processed: 178 average time/residue: 1.0452 time to fit residues: 196.9626 Evaluate side-chains 107 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 134 ASN A 161 GLN A 390 GLN A 398 GLN A 569 HIS A 805 HIS A 906 HIS ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN A 968 GLN A 971 HIS A1157 ASN A1214 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.202356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.172221 restraints weight = 11921.854| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 3.85 r_work: 0.4485 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6871 Z= 0.320 Angle : 0.731 9.872 9339 Z= 0.366 Chirality : 0.045 0.179 1004 Planarity : 0.005 0.056 1214 Dihedral : 4.613 35.880 928 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.26 % Allowed : 14.33 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.20 (0.29), residues: 837 helix: 0.79 (0.27), residues: 347 sheet: 0.57 (0.57), residues: 83 loop : -0.46 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 918 HIS 0.007 0.002 HIS A 84 PHE 0.013 0.002 PHE A 197 TYR 0.031 0.002 TYR A 452 ARG 0.005 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 TYR cc_start: 0.6712 (t80) cc_final: 0.5798 (t80) REVERT: A 831 TYR cc_start: 0.7502 (t80) cc_final: 0.7291 (t80) REVERT: A 907 PHE cc_start: 0.7140 (t80) cc_final: 0.6668 (t80) REVERT: A 1057 MET cc_start: 0.5044 (OUTLIER) cc_final: 0.4758 (pp-130) REVERT: A 1108 TYR cc_start: 0.7773 (t80) cc_final: 0.7508 (t80) REVERT: A 1153 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5676 (mp) outliers start: 30 outliers final: 10 residues processed: 125 average time/residue: 1.0738 time to fit residues: 142.3541 Evaluate side-chains 97 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.0970 chunk 37 optimal weight: 0.0060 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 144 GLN ** A 971 HIS ** 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 = 0.5001 r_free = 0.5001 target = 0.204682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.174734 restraints weight = 11985.096| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 3.86 r_work: 0.4549 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6871 Z= 0.207 Angle : 0.691 15.665 9339 Z= 0.333 Chirality : 0.043 0.245 1004 Planarity : 0.005 0.055 1214 Dihedral : 4.426 33.562 925 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.70 % Allowed : 17.45 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.35 (0.29), residues: 837 helix: 0.93 (0.27), residues: 356 sheet: 0.35 (0.55), residues: 89 loop : -0.35 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 585 HIS 0.005 0.001 HIS A 84 PHE 0.008 0.001 PHE A 800 TYR 0.014 0.002 TYR A1166 ARG 0.007 0.001 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7067 (tp30) REVERT: A 429 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: A 444 TYR cc_start: 0.6542 (t80) cc_final: 0.5635 (t80) REVERT: A 452 TYR cc_start: 0.7749 (t80) cc_final: 0.7544 (t80) REVERT: A 774 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5799 (mpp) REVERT: A 831 TYR cc_start: 0.7420 (t80) cc_final: 0.7201 (t80) REVERT: A 874 LEU cc_start: 0.7776 (tp) cc_final: 0.7534 (tp) REVERT: A 877 MET cc_start: 0.7860 (tpp) cc_final: 0.7611 (mpp) REVERT: A 907 PHE cc_start: 0.7025 (t80) cc_final: 0.6680 (t80) REVERT: A 1062 GLU cc_start: 0.6084 (mm-30) cc_final: 0.4235 (pp20) REVERT: A 1153 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5431 (mp) REVERT: A 1163 MET cc_start: 0.5501 (tmm) cc_final: 0.4847 (tpt) outliers start: 19 outliers final: 5 residues processed: 110 average time/residue: 1.1473 time to fit residues: 133.5645 Evaluate side-chains 91 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 971 HIS ** 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 = 0.4974 r_free = 0.4974 target = 0.204136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.173419 restraints weight = 12015.974| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 4.05 r_work: 0.4488 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6871 Z= 0.219 Angle : 0.691 14.268 9339 Z= 0.330 Chirality : 0.044 0.200 1004 Planarity : 0.005 0.055 1214 Dihedral : 4.505 30.304 925 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.84 % Allowed : 19.29 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.32 (0.29), residues: 837 helix: 0.85 (0.28), residues: 357 sheet: 0.21 (0.56), residues: 86 loop : -0.28 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 607 HIS 0.014 0.001 HIS A 971 PHE 0.011 0.001 PHE A 273 TYR 0.012 0.001 TYR A1166 ARG 0.008 0.001 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7062 (tp30) REVERT: A 444 TYR cc_start: 0.6746 (t80) cc_final: 0.6002 (t80) REVERT: A 449 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.6469 (pp30) REVERT: A 774 MET cc_start: 0.6080 (mpp) cc_final: 0.5880 (mpp) REVERT: A 831 TYR cc_start: 0.7570 (t80) cc_final: 0.7350 (t80) REVERT: A 907 PHE cc_start: 0.7001 (t80) cc_final: 0.6638 (t80) REVERT: A 1058 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6136 (m-80) REVERT: A 1062 GLU cc_start: 0.5997 (mm-30) cc_final: 0.4166 (pp20) REVERT: A 1153 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5111 (mp) REVERT: A 1163 MET cc_start: 0.5208 (tmm) cc_final: 0.4581 (tpt) outliers start: 20 outliers final: 9 residues processed: 109 average time/residue: 0.9565 time to fit residues: 111.5542 Evaluate side-chains 94 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 894 GLN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.202579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.171477 restraints weight = 11840.724| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 4.00 r_work: 0.4465 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6871 Z= 0.265 Angle : 0.744 13.365 9339 Z= 0.354 Chirality : 0.045 0.177 1004 Planarity : 0.005 0.057 1214 Dihedral : 4.608 30.882 925 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.12 % Allowed : 20.14 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.15 (0.29), residues: 837 helix: 0.76 (0.28), residues: 355 sheet: -0.09 (0.57), residues: 86 loop : -0.37 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 607 HIS 0.013 0.001 HIS A 971 PHE 0.031 0.002 PHE A 139 TYR 0.012 0.002 TYR A1166 ARG 0.005 0.001 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7132 (tp30) REVERT: A 449 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6311 (pp30) REVERT: A 464 MET cc_start: 0.9348 (ptm) cc_final: 0.8889 (tmm) REVERT: A 831 TYR cc_start: 0.7651 (t80) cc_final: 0.7449 (t80) REVERT: A 904 ASP cc_start: 0.5485 (m-30) cc_final: 0.5269 (m-30) REVERT: A 907 PHE cc_start: 0.7059 (t80) cc_final: 0.6676 (t80) REVERT: A 910 MET cc_start: 0.5706 (mtp) cc_final: 0.4917 (ttp) REVERT: A 1058 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6173 (m-80) REVERT: A 1062 GLU cc_start: 0.6058 (mm-30) cc_final: 0.4203 (pp20) REVERT: A 1093 MET cc_start: 0.3251 (tpp) cc_final: 0.2988 (tpp) REVERT: A 1153 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5344 (mp) REVERT: A 1163 MET cc_start: 0.5356 (tmm) cc_final: 0.4755 (tpt) outliers start: 22 outliers final: 10 residues processed: 109 average time/residue: 0.9273 time to fit residues: 107.9732 Evaluate side-chains 95 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.202742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.172591 restraints weight = 11842.681| |-----------------------------------------------------------------------------| r_work (start): 0.4660 rms_B_bonded: 3.79 r_work: 0.4511 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6871 Z= 0.215 Angle : 0.719 18.319 9339 Z= 0.339 Chirality : 0.045 0.347 1004 Planarity : 0.005 0.058 1214 Dihedral : 4.520 27.385 925 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.70 % Allowed : 21.99 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.22 (0.30), residues: 837 helix: 0.84 (0.28), residues: 355 sheet: -0.19 (0.58), residues: 81 loop : -0.32 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 748 HIS 0.012 0.001 HIS A 971 PHE 0.013 0.001 PHE A 139 TYR 0.019 0.001 TYR A 444 ARG 0.004 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7158 (tp30) REVERT: A 430 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5344 (ttm) REVERT: A 449 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.6109 (pp30) REVERT: A 774 MET cc_start: 0.5611 (mpp) cc_final: 0.5177 (mpp) REVERT: A 907 PHE cc_start: 0.7051 (t80) cc_final: 0.6736 (t80) REVERT: A 910 MET cc_start: 0.6030 (mtp) cc_final: 0.5122 (ttp) REVERT: A 986 TYR cc_start: 0.6566 (m-80) cc_final: 0.3805 (m-80) REVERT: A 1058 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: A 1062 GLU cc_start: 0.6062 (mm-30) cc_final: 0.4214 (pp20) REVERT: A 1153 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5574 (mp) REVERT: A 1163 MET cc_start: 0.5566 (tmm) cc_final: 0.4967 (tpt) outliers start: 19 outliers final: 8 residues processed: 103 average time/residue: 0.9733 time to fit residues: 106.9269 Evaluate side-chains 97 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** 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 = 0.4980 r_free = 0.4980 target = 0.202687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.172803 restraints weight = 11904.093| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 3.77 r_work: 0.4510 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6871 Z= 0.208 Angle : 0.748 16.607 9339 Z= 0.348 Chirality : 0.046 0.190 1004 Planarity : 0.005 0.056 1214 Dihedral : 4.492 26.429 925 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.12 % Allowed : 22.13 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 837 helix: 0.74 (0.27), residues: 359 sheet: -0.15 (0.59), residues: 81 loop : -0.24 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 748 HIS 0.002 0.000 HIS A 298 PHE 0.025 0.001 PHE A 139 TYR 0.027 0.002 TYR A 444 ARG 0.006 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7190 (tp30) REVERT: A 429 GLU cc_start: 0.6124 (mp0) cc_final: 0.5891 (mp0) REVERT: A 430 MET cc_start: 0.5628 (OUTLIER) cc_final: 0.5293 (ttm) REVERT: A 449 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5953 (pp30) REVERT: A 798 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7474 (pp) REVERT: A 907 PHE cc_start: 0.6980 (t80) cc_final: 0.6688 (t80) REVERT: A 910 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5652 (ttp) REVERT: A 985 MET cc_start: 0.7524 (tmm) cc_final: 0.6579 (ppp) REVERT: A 986 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.4123 (m-80) REVERT: A 1058 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: A 1062 GLU cc_start: 0.5987 (mm-30) cc_final: 0.4187 (pp20) REVERT: A 1153 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5623 (mp) REVERT: A 1163 MET cc_start: 0.5512 (tmm) cc_final: 0.4932 (tpt) REVERT: A 1206 MET cc_start: 0.7061 (tmt) cc_final: 0.6805 (tmt) outliers start: 22 outliers final: 9 residues processed: 102 average time/residue: 1.0204 time to fit residues: 110.8337 Evaluate side-chains 98 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 986 TYR Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** 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 = 0.4962 r_free = 0.4962 target = 0.200488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.170382 restraints weight = 11784.374| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 3.74 r_work: 0.4480 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6871 Z= 0.259 Angle : 0.796 18.083 9339 Z= 0.368 Chirality : 0.046 0.270 1004 Planarity : 0.005 0.059 1214 Dihedral : 4.607 26.160 925 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.12 % Allowed : 23.40 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.12 (0.29), residues: 837 helix: 0.67 (0.27), residues: 358 sheet: -0.05 (0.61), residues: 71 loop : -0.34 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 748 HIS 0.003 0.001 HIS A 298 PHE 0.021 0.002 PHE A 139 TYR 0.024 0.002 TYR A 444 ARG 0.005 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7188 (tp30) REVERT: A 429 GLU cc_start: 0.6271 (mp0) cc_final: 0.6030 (mp0) REVERT: A 430 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.5298 (ttm) REVERT: A 449 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6095 (pp30) REVERT: A 597 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7353 (mmt180) REVERT: A 603 MET cc_start: 0.7307 (pmm) cc_final: 0.7078 (ppp) REVERT: A 907 PHE cc_start: 0.7046 (t80) cc_final: 0.6697 (t80) REVERT: A 910 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5756 (ttp) REVERT: A 985 MET cc_start: 0.7656 (tmm) cc_final: 0.6789 (ppp) REVERT: A 986 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.4228 (m-80) REVERT: A 1058 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.6286 (m-80) REVERT: A 1062 GLU cc_start: 0.5946 (mm-30) cc_final: 0.4109 (pp20) REVERT: A 1153 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5717 (mp) REVERT: A 1163 MET cc_start: 0.5629 (tmm) cc_final: 0.5022 (tpt) REVERT: A 1206 MET cc_start: 0.7167 (tmt) cc_final: 0.6845 (tmt) outliers start: 22 outliers final: 9 residues processed: 98 average time/residue: 0.9777 time to fit residues: 102.5229 Evaluate side-chains 98 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 986 TYR Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** 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 = 0.4903 r_free = 0.4903 target = 0.199508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.166861 restraints weight = 12067.908| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 4.03 r_work: 0.4385 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6871 Z= 0.265 Angle : 0.801 17.614 9339 Z= 0.375 Chirality : 0.047 0.283 1004 Planarity : 0.005 0.058 1214 Dihedral : 4.608 26.075 924 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 3.55 % Allowed : 23.12 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.04 (0.29), residues: 837 helix: 0.56 (0.27), residues: 352 sheet: -0.11 (0.61), residues: 71 loop : -0.42 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 748 HIS 0.003 0.001 HIS A 277 PHE 0.019 0.002 PHE A 139 TYR 0.026 0.002 TYR A 444 ARG 0.007 0.001 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7167 (tp30) REVERT: A 429 GLU cc_start: 0.6050 (mp0) cc_final: 0.5824 (mp0) REVERT: A 430 MET cc_start: 0.5606 (OUTLIER) cc_final: 0.5292 (ttm) REVERT: A 449 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6148 (pp30) REVERT: A 464 MET cc_start: 0.8908 (ptp) cc_final: 0.8582 (tmm) REVERT: A 597 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7591 (mmt180) REVERT: A 774 MET cc_start: 0.5262 (mpp) cc_final: 0.5023 (mmm) REVERT: A 798 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7518 (pp) REVERT: A 907 PHE cc_start: 0.7062 (t80) cc_final: 0.6643 (t80) REVERT: A 910 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5547 (ttp) REVERT: A 985 MET cc_start: 0.7782 (tmm) cc_final: 0.6935 (ppp) REVERT: A 986 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.4353 (m-80) REVERT: A 1062 GLU cc_start: 0.5910 (mm-30) cc_final: 0.3769 (pt0) REVERT: A 1153 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5689 (mt) REVERT: A 1163 MET cc_start: 0.5593 (tmm) cc_final: 0.4973 (tpt) REVERT: A 1206 MET cc_start: 0.7073 (tmt) cc_final: 0.6857 (tmt) outliers start: 25 outliers final: 11 residues processed: 97 average time/residue: 0.9605 time to fit residues: 99.6233 Evaluate side-chains 100 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 986 TYR Chi-restraints excluded: chain A residue 1080 SER Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN ** A 932 HIS ** 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 = 0.4932 r_free = 0.4932 target = 0.199616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.168680 restraints weight = 12223.849| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 4.00 r_work: 0.4462 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6871 Z= 0.263 Angle : 0.831 17.048 9339 Z= 0.383 Chirality : 0.048 0.284 1004 Planarity : 0.005 0.058 1214 Dihedral : 4.654 26.118 924 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 2.98 % Allowed : 23.55 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.17 (0.29), residues: 837 helix: 0.51 (0.27), residues: 357 sheet: -0.55 (0.59), residues: 81 loop : -0.49 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 748 HIS 0.003 0.001 HIS A 277 PHE 0.017 0.001 PHE A 139 TYR 0.031 0.002 TYR A 444 ARG 0.009 0.001 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.6069 (mp0) cc_final: 0.5847 (mp0) REVERT: A 430 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.5157 (ttm) REVERT: A 449 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6354 (pp30) REVERT: A 597 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7400 (mmt180) REVERT: A 774 MET cc_start: 0.5203 (mpp) cc_final: 0.4971 (mmm) REVERT: A 798 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7524 (pp) REVERT: A 907 PHE cc_start: 0.7038 (t80) cc_final: 0.6651 (t80) REVERT: A 910 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5849 (ttp) REVERT: A 985 MET cc_start: 0.7715 (tmm) cc_final: 0.6912 (ppp) REVERT: A 986 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.4242 (m-80) REVERT: A 1062 GLU cc_start: 0.5841 (mm-30) cc_final: 0.3771 (pt0) REVERT: A 1153 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5744 (mp) REVERT: A 1163 MET cc_start: 0.5547 (tmm) cc_final: 0.4913 (tpt) REVERT: A 1206 MET cc_start: 0.7093 (tmt) cc_final: 0.6848 (tmt) outliers start: 21 outliers final: 10 residues processed: 98 average time/residue: 1.0216 time to fit residues: 107.0108 Evaluate side-chains 97 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 986 TYR Chi-restraints excluded: chain A residue 1080 SER Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 70 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 932 HIS ** 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 = 0.4941 r_free = 0.4941 target = 0.200521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.168023 restraints weight = 12406.253| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 4.22 r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 6871 Z= 0.282 Angle : 0.862 16.834 9339 Z= 0.403 Chirality : 0.049 0.289 1004 Planarity : 0.005 0.058 1214 Dihedral : 4.663 26.083 924 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.26 % Favored : 94.50 % Rotamer: Outliers : 3.12 % Allowed : 24.26 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.25 (0.29), residues: 837 helix: 0.44 (0.27), residues: 357 sheet: -0.70 (0.58), residues: 82 loop : -0.50 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 748 HIS 0.006 0.001 HIS A 420 PHE 0.016 0.001 PHE A 139 TYR 0.033 0.002 TYR A 444 ARG 0.007 0.001 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4612.50 seconds wall clock time: 79 minutes 25.70 seconds (4765.70 seconds total)