Starting phenix.real_space_refine on Tue Jan 14 14:44:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5d_42982/01_2025/8v5d_42982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5d_42982/01_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_42982/01_2025/8v5d_42982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5d_42982/01_2025/8v5d_42982.map" model { file = "/net/cci-nas-00/data/ceres_data/8v5d_42982/01_2025/8v5d_42982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5d_42982/01_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-5571/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: 4.48, per 1000 atoms: 0.67 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: 1.55 Conformation dependent library (CDL) restraints added in 950.9 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: 0.81 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: 2.30 Time building geometry restraints manager: 1.86 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: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.700 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- 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 : 0.661 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: 1.1383 time to fit residues: 213.9543 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 : 0.703 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.172187 restraints weight = 11921.854| |-----------------------------------------------------------------------------| r_work (start): 0.4646 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: 0.6183 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 : 0.710 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: 0.6708 (t80) cc_final: 0.5793 (t80) REVERT: A 831 TYR cc_start: 0.7502 (t80) cc_final: 0.7291 (t80) REVERT: A 907 PHE cc_start: 0.7143 (t80) cc_final: 0.6670 (t80) REVERT: A 1057 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4762 (pp-130) REVERT: A 1108 TYR cc_start: 0.7776 (t80) cc_final: 0.7510 (t80) REVERT: A 1153 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5671 (mp) outliers start: 30 outliers final: 10 residues processed: 125 average time/residue: 1.1662 time to fit residues: 154.3611 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 : 0.712 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.2980 chunk 44 optimal weight: 0.0270 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5002 r_free = 0.5002 target = 0.204467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.174500 restraints weight = 11955.783| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 3.91 r_work: 0.4552 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6871 Z= 0.202 Angle : 0.688 15.443 9339 Z= 0.332 Chirality : 0.043 0.268 1004 Planarity : 0.005 0.055 1214 Dihedral : 4.446 33.473 925 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.41 % Allowed : 17.87 % Favored : 79.72 % 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: 0.36 (0.29), residues: 837 helix: 0.93 (0.27), residues: 356 sheet: 0.41 (0.55), residues: 88 loop : -0.37 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 585 HIS 0.005 0.001 HIS A 971 PHE 0.007 0.001 PHE A 800 TYR 0.014 0.002 TYR A1166 ARG 0.008 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 115 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7082 (tp30) REVERT: A 398 GLN cc_start: 0.5238 (OUTLIER) cc_final: 0.4995 (pp30) REVERT: A 429 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6036 (mp0) REVERT: A 444 TYR cc_start: 0.6568 (t80) cc_final: 0.5794 (t80) REVERT: A 452 TYR cc_start: 0.7730 (t80) cc_final: 0.7496 (t80) REVERT: A 774 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5876 (mpp) REVERT: A 831 TYR cc_start: 0.7442 (t80) cc_final: 0.7224 (t80) REVERT: A 874 LEU cc_start: 0.7762 (tp) cc_final: 0.7533 (tp) REVERT: A 907 PHE cc_start: 0.7019 (t80) cc_final: 0.6674 (t80) REVERT: A 1062 GLU cc_start: 0.6037 (mm-30) cc_final: 0.4252 (pp20) REVERT: A 1153 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5482 (mp) REVERT: A 1163 MET cc_start: 0.5504 (tmm) cc_final: 0.4846 (tpt) outliers start: 17 outliers final: 5 residues processed: 110 average time/residue: 1.1118 time to fit residues: 129.5174 Evaluate side-chains 94 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 398 GLN 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: 3.9990 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4976 r_free = 0.4976 target = 0.204621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.174340 restraints weight = 12012.272| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 4.01 r_work: 0.4483 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6871 Z= 0.211 Angle : 0.693 14.358 9339 Z= 0.331 Chirality : 0.044 0.186 1004 Planarity : 0.005 0.052 1214 Dihedral : 4.489 29.942 925 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.26 % Allowed : 18.72 % Favored : 78.01 % 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 (0.30), residues: 837 helix: 0.79 (0.27), residues: 364 sheet: 0.12 (0.56), residues: 89 loop : -0.21 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 607 HIS 0.014 0.001 HIS A 971 PHE 0.010 0.001 PHE A 273 TYR 0.012 0.001 TYR A1166 ARG 0.009 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 116 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.715 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: 0.7690 (mt-10) cc_final: 0.7068 (tp30) REVERT: A 449 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6380 (pp30) REVERT: A 831 TYR cc_start: 0.7529 (t80) cc_final: 0.7306 (t80) REVERT: A 877 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7509 (mmp) REVERT: A 907 PHE cc_start: 0.7006 (t80) cc_final: 0.6653 (t80) REVERT: A 910 MET cc_start: 0.5608 (mtp) cc_final: 0.5228 (ttp) REVERT: A 1058 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: A 1062 GLU cc_start: 0.5987 (mm-30) cc_final: 0.4166 (pp20) REVERT: A 1153 LEU cc_start: 0.5446 (OUTLIER) cc_final: 0.5109 (mp) REVERT: A 1163 MET cc_start: 0.5230 (tmm) cc_final: 0.4608 (tpt) outliers start: 23 outliers final: 9 residues processed: 109 average time/residue: 0.9879 time to fit residues: 114.7123 Evaluate side-chains 96 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 877 MET 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: 1.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 110 HIS ** 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 = 0.4984 r_free = 0.4984 target = 0.202814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.172100 restraints weight = 11978.666| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 3.91 r_work: 0.4507 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.3841 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= 0.222 Angle : 0.723 12.728 9339 Z= 0.342 Chirality : 0.044 0.147 1004 Planarity : 0.004 0.054 1214 Dihedral : 4.481 30.767 925 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.26 % Allowed : 19.86 % Favored : 76.88 % 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: 0.30 (0.30), residues: 837 helix: 0.81 (0.28), residues: 363 sheet: -0.04 (0.56), residues: 89 loop : -0.22 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 748 HIS 0.013 0.001 HIS A 971 PHE 0.024 0.001 PHE A 139 TYR 0.015 0.001 TYR A 444 ARG 0.004 0.000 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 113 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.736 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: 0.7754 (mt-10) cc_final: 0.7193 (tp30) REVERT: A 449 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.6026 (pp30) REVERT: A 774 MET cc_start: 0.5681 (mpp) cc_final: 0.5254 (mpp) REVERT: A 831 TYR cc_start: 0.7449 (t80) cc_final: 0.7244 (t80) REVERT: A 877 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7576 (mpp) REVERT: A 907 PHE cc_start: 0.7009 (t80) cc_final: 0.6713 (t80) REVERT: A 910 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5629 (ttp) REVERT: A 1058 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: A 1062 GLU cc_start: 0.6067 (mm-30) cc_final: 0.4246 (pp20) REVERT: A 1153 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5531 (mp) REVERT: A 1163 MET cc_start: 0.5670 (tmm) cc_final: 0.5003 (tpt) outliers start: 23 outliers final: 10 residues processed: 105 average time/residue: 1.0486 time to fit residues: 117.2548 Evaluate side-chains 94 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 597 ARG Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1058 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.0020 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 110 HIS A 894 GLN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4988 r_free = 0.4988 target = 0.202987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.172772 restraints weight = 11875.846| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 3.79 r_work: 0.4519 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6871 Z= 0.230 Angle : 0.728 16.140 9339 Z= 0.344 Chirality : 0.045 0.310 1004 Planarity : 0.005 0.061 1214 Dihedral : 4.535 27.911 925 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.12 % Allowed : 20.99 % Favored : 75.89 % 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: 0.24 (0.30), residues: 837 helix: 0.78 (0.28), residues: 362 sheet: -0.04 (0.58), residues: 81 loop : -0.27 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 748 HIS 0.012 0.001 HIS A 971 PHE 0.016 0.001 PHE A 139 TYR 0.011 0.001 TYR A1166 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: 22 poor density : 85 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7186 (tp30) REVERT: A 449 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.6042 (pp30) REVERT: A 464 MET cc_start: 0.8957 (ptp) cc_final: 0.8632 (tmm) REVERT: A 774 MET cc_start: 0.5565 (mpp) cc_final: 0.5073 (mmm) REVERT: A 907 PHE cc_start: 0.7011 (t80) cc_final: 0.6704 (t80) REVERT: A 910 MET cc_start: 0.6072 (OUTLIER) cc_final: 0.5137 (ttp) REVERT: A 1058 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: A 1062 GLU cc_start: 0.6052 (mm-30) cc_final: 0.4249 (pp20) REVERT: A 1153 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5523 (mp) REVERT: A 1163 MET cc_start: 0.5576 (tmm) cc_final: 0.4979 (tpt) outliers start: 22 outliers final: 9 residues processed: 100 average time/residue: 1.0606 time to fit residues: 112.7243 Evaluate side-chains 91 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 1058 PHE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.0060 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 110 HIS ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4993 r_free = 0.4993 target = 0.204014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.172863 restraints weight = 12120.903| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 3.92 r_work: 0.4534 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6871 Z= 0.199 Angle : 0.730 18.700 9339 Z= 0.338 Chirality : 0.044 0.167 1004 Planarity : 0.005 0.057 1214 Dihedral : 4.486 27.278 925 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.12 % Allowed : 21.84 % Favored : 75.04 % 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: 0.29 (0.30), residues: 837 helix: 0.80 (0.27), residues: 365 sheet: -0.06 (0.59), residues: 81 loop : -0.21 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 748 HIS 0.011 0.001 HIS A 971 PHE 0.022 0.001 PHE A 139 TYR 0.011 0.001 TYR A1166 ARG 0.007 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 112 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.6416 (tm) cc_final: 0.6102 (pt) REVERT: A 375 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7173 (tp30) REVERT: A 429 GLU cc_start: 0.6337 (mp0) cc_final: 0.6046 (mp0) REVERT: A 449 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5976 (pp30) REVERT: A 464 MET cc_start: 0.8915 (ptp) cc_final: 0.8601 (tmm) REVERT: A 774 MET cc_start: 0.5511 (mpp) cc_final: 0.4971 (mmm) REVERT: A 798 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7425 (pp) REVERT: A 877 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7455 (mpp) REVERT: A 907 PHE cc_start: 0.6973 (t80) cc_final: 0.6675 (t80) REVERT: A 985 MET cc_start: 0.7447 (tmm) cc_final: 0.6336 (ppp) REVERT: A 986 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.4231 (m-80) REVERT: A 1058 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: A 1062 GLU cc_start: 0.6001 (mm-30) cc_final: 0.4243 (pp20) REVERT: A 1153 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5620 (mp) REVERT: A 1163 MET cc_start: 0.5524 (tmm) cc_final: 0.4752 (tpt) REVERT: A 1206 MET cc_start: 0.7186 (tmt) cc_final: 0.6801 (tmt) outliers start: 22 outliers final: 7 residues processed: 103 average time/residue: 1.0863 time to fit residues: 119.5363 Evaluate side-chains 93 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 877 MET Chi-restraints excluded: chain A residue 986 TYR Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 410 GLN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 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 = 0.4849 r_free = 0.4849 target = 0.194283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.161829 restraints weight = 11933.758| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 3.95 r_work: 0.4325 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 6871 Z= 0.410 Angle : 0.902 16.495 9339 Z= 0.433 Chirality : 0.051 0.418 1004 Planarity : 0.006 0.065 1214 Dihedral : 5.012 26.772 923 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.33 % Favored : 93.55 % Rotamer: Outliers : 3.83 % Allowed : 22.70 % 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: -0.49 (0.29), residues: 837 helix: 0.15 (0.27), residues: 356 sheet: -0.49 (0.60), residues: 78 loop : -0.61 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 748 HIS 0.011 0.002 HIS A 971 PHE 0.034 0.003 PHE A 139 TYR 0.017 0.003 TYR A 221 ARG 0.006 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 113 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.6920 (m) cc_final: 0.6633 (p) REVERT: A 228 LEU cc_start: 0.6330 (tm) cc_final: 0.6055 (pt) REVERT: A 429 GLU cc_start: 0.6286 (mp0) cc_final: 0.6066 (mp0) REVERT: A 430 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.5337 (ttm) REVERT: A 449 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6369 (pp30) REVERT: A 603 MET cc_start: 0.7436 (pmm) cc_final: 0.7157 (ppp) REVERT: A 798 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7487 (pp) REVERT: A 877 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: A 907 PHE cc_start: 0.7168 (t80) cc_final: 0.6695 (t80) REVERT: A 985 MET cc_start: 0.7838 (tmm) cc_final: 0.6875 (pp-130) REVERT: A 986 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.3979 (m-80) REVERT: A 1062 GLU cc_start: 0.5836 (mm-30) cc_final: 0.3861 (pp20) REVERT: A 1153 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5841 (mt) REVERT: A 1163 MET cc_start: 0.5719 (tmm) cc_final: 0.5050 (tpt) REVERT: A 1206 MET cc_start: 0.7082 (tmt) cc_final: 0.6707 (tmt) outliers start: 27 outliers final: 14 residues processed: 101 average time/residue: 0.8979 time to fit residues: 97.4486 Evaluate side-chains 99 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 986 TYR Chi-restraints excluded: chain A residue 1058 PHE 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 Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 79 optimal weight: 0.0770 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 110 HIS A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.199795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.167961 restraints weight = 12034.207| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 3.98 r_work: 0.4404 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6871 Z= 0.227 Angle : 0.807 18.667 9339 Z= 0.381 Chirality : 0.047 0.172 1004 Planarity : 0.005 0.058 1214 Dihedral : 4.756 26.841 923 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.06 % Favored : 95.82 % Rotamer: Outliers : 2.41 % Allowed : 25.25 % Favored : 72.34 % 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: -0.26 (0.29), residues: 837 helix: 0.35 (0.27), residues: 356 sheet: -0.67 (0.58), residues: 83 loop : -0.42 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 748 HIS 0.011 0.001 HIS A 971 PHE 0.026 0.001 PHE A 949 TYR 0.014 0.001 TYR A 831 ARG 0.008 0.001 ARG A 227 *********************** 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 101 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.6988 (m) cc_final: 0.6688 (p) REVERT: A 375 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7165 (tp30) REVERT: A 429 GLU cc_start: 0.6132 (mp0) cc_final: 0.5914 (mp0) REVERT: A 430 MET cc_start: 0.5657 (OUTLIER) cc_final: 0.5342 (ttm) REVERT: A 449 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.6026 (pp30) REVERT: A 774 MET cc_start: 0.5227 (mpp) cc_final: 0.4878 (mmm) REVERT: A 798 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7372 (pp) REVERT: A 877 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7406 (mpp) REVERT: A 907 PHE cc_start: 0.7032 (t80) cc_final: 0.6614 (t80) REVERT: A 985 MET cc_start: 0.7817 (tmm) cc_final: 0.6972 (ppp) REVERT: A 986 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.4134 (m-80) REVERT: A 1058 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: A 1062 GLU cc_start: 0.5957 (mm-30) cc_final: 0.3834 (pt0) REVERT: A 1163 MET cc_start: 0.5552 (tmm) cc_final: 0.4939 (tpt) REVERT: A 1206 MET cc_start: 0.7087 (tmt) cc_final: 0.6859 (tmt) outliers start: 17 outliers final: 5 residues processed: 92 average time/residue: 1.0090 time to fit residues: 99.2551 Evaluate side-chains 90 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 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 1184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.202024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.169957 restraints weight = 12402.801| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 3.98 r_work: 0.4485 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6871 Z= 0.243 Angle : 0.821 18.028 9339 Z= 0.384 Chirality : 0.049 0.454 1004 Planarity : 0.005 0.059 1214 Dihedral : 4.676 27.276 922 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 1.84 % Allowed : 25.67 % Favored : 72.48 % 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: -0.28 (0.29), residues: 837 helix: 0.34 (0.27), residues: 357 sheet: -0.70 (0.58), residues: 83 loop : -0.43 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 748 HIS 0.011 0.001 HIS A 420 PHE 0.021 0.002 PHE A 949 TYR 0.013 0.001 TYR A 831 ARG 0.006 0.000 ARG A 288 ********************** 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 97 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.6928 (m) cc_final: 0.6708 (p) REVERT: A 375 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7194 (tp30) REVERT: A 429 GLU cc_start: 0.6286 (mp0) cc_final: 0.6061 (mp0) REVERT: A 449 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.5960 (pp30) REVERT: A 774 MET cc_start: 0.5218 (mpp) cc_final: 0.4824 (mmm) REVERT: A 798 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7369 (pp) REVERT: A 877 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7243 (mpp) REVERT: A 907 PHE cc_start: 0.6997 (t80) cc_final: 0.6609 (t80) REVERT: A 985 MET cc_start: 0.7809 (tmm) cc_final: 0.6986 (ppp) REVERT: A 986 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.4190 (m-80) REVERT: A 1058 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: A 1062 GLU cc_start: 0.5961 (mm-30) cc_final: 0.3876 (pt0) REVERT: A 1163 MET cc_start: 0.5711 (tmm) cc_final: 0.5082 (tpt) REVERT: A 1206 MET cc_start: 0.7104 (tmt) cc_final: 0.6897 (tmt) outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 1.0606 time to fit residues: 101.7013 Evaluate side-chains 91 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 877 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 1155 ILE 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: 1.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 0.0370 overall best weight: 1.1062 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.201236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.170059 restraints weight = 12046.273| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 3.97 r_work: 0.4452 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6871 Z= 0.278 Angle : 0.850 17.384 9339 Z= 0.400 Chirality : 0.049 0.447 1004 Planarity : 0.005 0.060 1214 Dihedral : 4.701 26.554 922 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 2.84 % Allowed : 24.54 % 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: -0.39 (0.29), residues: 837 helix: 0.27 (0.27), residues: 356 sheet: -0.78 (0.58), residues: 83 loop : -0.51 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 748 HIS 0.011 0.001 HIS A 971 PHE 0.020 0.002 PHE A 949 TYR 0.015 0.001 TYR A 831 ARG 0.008 0.001 ARG A 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4675.78 seconds wall clock time: 83 minutes 19.72 seconds (4999.72 seconds total)