Starting phenix.real_space_refine on Wed Mar 12 22:31:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq8_38569/03_2025/8xq8_38569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq8_38569/03_2025/8xq8_38569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xq8_38569/03_2025/8xq8_38569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq8_38569/03_2025/8xq8_38569.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq8_38569/03_2025/8xq8_38569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq8_38569/03_2025/8xq8_38569.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 46 5.16 5 C 5423 2.51 5 N 1380 2.21 5 O 1469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8319 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 32, 'TRANS': 1018} Chain breaks: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.63 Number of scatterers: 8319 At special positions: 0 Unit cell: (78.84, 111.24, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 1 15.00 O 1469 8.00 N 1380 7.00 C 5423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 74.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.991A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.824A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.707A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.932A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.652A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 406 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.686A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.415A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.738A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.627A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.940A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.148A pdb=" N CYS A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 705 removed outlier: 4.028A pdb=" N VAL A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 727 through 754 removed outlier: 3.847A pdb=" N LEU A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 761 through 784 Processing helix chain 'A' and resid 795 through 858 removed outlier: 4.347A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 5.524A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.701A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 960 through 964 removed outlier: 4.145A pdb=" N ALA A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 removed outlier: 3.559A pdb=" N LYS A1050 " --> pdb=" O GLY A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1085 through 1108 Proline residue: A1101 - end of helix removed outlier: 3.785A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.587A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.867A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.500A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A1034 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A1010 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.531A pdb=" N TYR A1125 " --> pdb=" O VAL A1188 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A1188 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1189 " --> pdb=" O ASP A1144 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 3.590A pdb=" N ASN A1154 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A1159 " --> pdb=" O ASN A1154 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2003 1.33 - 1.46: 1873 1.46 - 1.58: 4518 1.58 - 1.70: 5 1.70 - 1.83: 83 Bond restraints: 8482 Sorted by residual: bond pdb=" O2P CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 1.510 1.643 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C4 CMP A2001 " pdb=" C5 CMP A2001 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C6 CMP A2001 " pdb=" N6 CMP A2001 " ideal model delta sigma weight residual 1.355 1.452 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C5 CMP A2001 " pdb=" C6 CMP A2001 " ideal model delta sigma weight residual 1.490 1.421 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O1P CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 1.510 1.452 0.058 2.00e-02 2.50e+03 8.27e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 11293 3.81 - 7.63: 172 7.63 - 11.44: 33 11.44 - 15.25: 7 15.25 - 19.07: 1 Bond angle restraints: 11506 Sorted by residual: angle pdb=" CG1 ILE A 652 " pdb=" CB ILE A 652 " pdb=" CG2 ILE A 652 " ideal model delta sigma weight residual 110.70 91.63 19.07 3.00e+00 1.11e-01 4.04e+01 angle pdb=" CA MET A 565 " pdb=" CB MET A 565 " pdb=" CG MET A 565 " ideal model delta sigma weight residual 114.10 125.72 -11.62 2.00e+00 2.50e-01 3.37e+01 angle pdb=" C SER A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 120.24 123.56 -3.32 6.30e-01 2.52e+00 2.77e+01 angle pdb=" CA GLN A1106 " pdb=" CB GLN A1106 " pdb=" CG GLN A1106 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" CB GLN A1106 " pdb=" CG GLN A1106 " pdb=" CD GLN A1106 " ideal model delta sigma weight residual 112.60 121.09 -8.49 1.70e+00 3.46e-01 2.49e+01 ... (remaining 11501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.26: 4686 26.26 - 52.53: 347 52.53 - 78.79: 32 78.79 - 105.06: 7 105.06 - 131.32: 1 Dihedral angle restraints: 5073 sinusoidal: 2016 harmonic: 3057 Sorted by residual: dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR A1049 " pdb=" C THR A1049 " pdb=" N LYS A1050 " pdb=" CA LYS A1050 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 754 " pdb=" C LEU A 754 " pdb=" N GLY A 755 " pdb=" CA GLY A 755 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1148 0.073 - 0.145: 186 0.145 - 0.218: 38 0.218 - 0.290: 4 0.290 - 0.363: 4 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB ILE A 652 " pdb=" CA ILE A 652 " pdb=" CG1 ILE A 652 " pdb=" CG2 ILE A 652 " both_signs ideal model delta sigma weight residual False 2.64 3.01 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB VAL A 116 " pdb=" CA VAL A 116 " pdb=" CG1 VAL A 116 " pdb=" CG2 VAL A 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1377 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 766 " 0.044 2.00e-02 2.50e+03 4.05e-02 2.87e+01 pdb=" CG PHE A 766 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE A 766 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 766 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 766 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 766 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 766 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1123 " -0.352 9.50e-02 1.11e+02 1.58e-01 1.64e+01 pdb=" NE ARG A1123 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A1123 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A1123 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A1123 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO A 276 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.042 5.00e-02 4.00e+02 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1782 2.78 - 3.31: 8007 3.31 - 3.84: 14026 3.84 - 4.37: 15109 4.37 - 4.90: 26778 Nonbonded interactions: 65702 Sorted by model distance: nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.255 3.040 nonbonded pdb=" O SER A 735 " pdb=" OG SER A 735 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU A 954 " pdb=" OH TYR A1066 " model vdw 2.280 3.040 nonbonded pdb=" O PHE A 680 " pdb=" OG1 THR A 683 " model vdw 2.302 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.306 3.040 ... (remaining 65697 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: 1.280 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 : 0.007 0.133 8482 Z= 0.404 Angle : 1.245 19.067 11506 Z= 0.646 Chirality : 0.061 0.363 1380 Planarity : 0.010 0.158 1415 Dihedral : 17.539 131.319 3091 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.77 % Allowed : 29.61 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1039 helix: -0.78 (0.16), residues: 755 sheet: -0.54 (0.69), residues: 50 loop : -1.26 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 427 HIS 0.024 0.002 HIS A1156 PHE 0.092 0.003 PHE A 766 TYR 0.045 0.002 TYR A 267 ARG 0.018 0.002 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 256 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8231 (p) cc_final: 0.8025 (m) REVERT: A 174 LEU cc_start: 0.8155 (tp) cc_final: 0.7821 (tp) REVERT: A 263 GLN cc_start: 0.7713 (mt0) cc_final: 0.7115 (mp10) REVERT: A 295 ASN cc_start: 0.8131 (t0) cc_final: 0.7609 (t0) REVERT: A 354 GLU cc_start: 0.7987 (tt0) cc_final: 0.7632 (tm-30) REVERT: A 621 GLU cc_start: 0.7384 (tp30) cc_final: 0.7176 (tp30) REVERT: A 671 MET cc_start: 0.7143 (mtt) cc_final: 0.6775 (mtt) REVERT: A 940 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7810 (ttm-80) REVERT: A 1008 LEU cc_start: 0.7198 (tt) cc_final: 0.6981 (tp) REVERT: A 1161 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7020 (pt) outliers start: 7 outliers final: 3 residues processed: 260 average time/residue: 0.2387 time to fit residues: 81.5768 Evaluate side-chains 248 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 44 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 292 HIS A 295 ASN A 624 GLN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A 955 ASN A1054 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118395 restraints weight = 13358.592| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.02 r_work: 0.3382 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8482 Z= 0.202 Angle : 0.655 14.579 11506 Z= 0.331 Chirality : 0.042 0.213 1380 Planarity : 0.005 0.056 1415 Dihedral : 6.327 135.268 1139 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.31 % Allowed : 23.76 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.25), residues: 1039 helix: 0.75 (0.18), residues: 752 sheet: -0.31 (0.68), residues: 48 loop : -0.87 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 635 HIS 0.005 0.001 HIS A 157 PHE 0.029 0.001 PHE A 766 TYR 0.018 0.001 TYR A 267 ARG 0.010 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8329 (p) cc_final: 0.7996 (m) REVERT: A 155 ASP cc_start: 0.7805 (t0) cc_final: 0.7547 (t0) REVERT: A 174 LEU cc_start: 0.8116 (tp) cc_final: 0.7696 (tp) REVERT: A 179 VAL cc_start: 0.7990 (t) cc_final: 0.7519 (p) REVERT: A 199 MET cc_start: 0.7658 (mpp) cc_final: 0.7438 (mpp) REVERT: A 229 ILE cc_start: 0.8038 (mm) cc_final: 0.7820 (mm) REVERT: A 250 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7561 (mttp) REVERT: A 258 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7199 (p) REVERT: A 295 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7387 (t0) REVERT: A 337 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6953 (tm-30) REVERT: A 381 ASP cc_start: 0.7328 (m-30) cc_final: 0.7100 (m-30) REVERT: A 389 ILE cc_start: 0.8198 (mt) cc_final: 0.7942 (mm) REVERT: A 443 GLU cc_start: 0.7966 (tp30) cc_final: 0.7527 (tp30) REVERT: A 671 MET cc_start: 0.7304 (mtt) cc_final: 0.7023 (mtt) REVERT: A 678 MET cc_start: 0.6642 (tpp) cc_final: 0.6325 (mpp) REVERT: A 681 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 684 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8596 (tp) REVERT: A 810 MET cc_start: 0.5835 (tmm) cc_final: 0.5597 (tmm) REVERT: A 853 ILE cc_start: 0.8733 (tt) cc_final: 0.8468 (tp) REVERT: A 969 LEU cc_start: 0.8685 (tp) cc_final: 0.8427 (tp) REVERT: A 972 PHE cc_start: 0.8499 (t80) cc_final: 0.8271 (t80) REVERT: A 1087 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: A 1097 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7865 (ttp80) REVERT: A 1118 LYS cc_start: 0.7007 (tmtt) cc_final: 0.6673 (tmtt) REVERT: A 1190 ARG cc_start: 0.7532 (mpt180) cc_final: 0.7214 (mpt180) outliers start: 39 outliers final: 17 residues processed: 272 average time/residue: 0.2304 time to fit residues: 82.6601 Evaluate side-chains 262 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1087 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 HIS A 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 GLN A1135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112194 restraints weight = 13373.086| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.09 r_work: 0.3315 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8482 Z= 0.351 Angle : 0.683 14.155 11506 Z= 0.354 Chirality : 0.045 0.203 1380 Planarity : 0.005 0.052 1415 Dihedral : 6.253 133.811 1135 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.20 % Allowed : 23.54 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1039 helix: 1.07 (0.18), residues: 753 sheet: -0.17 (0.73), residues: 48 loop : -1.03 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 193 HIS 0.005 0.001 HIS A 350 PHE 0.020 0.002 PHE A 766 TYR 0.020 0.002 TYR A 267 ARG 0.010 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7570 (mt) REVERT: A 155 ASP cc_start: 0.7957 (t0) cc_final: 0.7642 (t0) REVERT: A 174 LEU cc_start: 0.8183 (tp) cc_final: 0.7921 (tp) REVERT: A 250 LYS cc_start: 0.8301 (mmmm) cc_final: 0.8026 (mttp) REVERT: A 258 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7216 (p) REVERT: A 337 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6844 (tm-30) REVERT: A 354 GLU cc_start: 0.8089 (tt0) cc_final: 0.7619 (tm-30) REVERT: A 383 MET cc_start: 0.6928 (mmm) cc_final: 0.6409 (mmm) REVERT: A 443 GLU cc_start: 0.7972 (tp30) cc_final: 0.7521 (tp30) REVERT: A 581 GLU cc_start: 0.7699 (tp30) cc_final: 0.7325 (tp30) REVERT: A 671 MET cc_start: 0.7372 (mtt) cc_final: 0.7165 (mtt) REVERT: A 678 MET cc_start: 0.6778 (tpp) cc_final: 0.6471 (mpp) REVERT: A 681 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 684 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8627 (tp) REVERT: A 775 LEU cc_start: 0.8189 (mt) cc_final: 0.7828 (mt) REVERT: A 810 MET cc_start: 0.6121 (tmm) cc_final: 0.5740 (tmm) REVERT: A 943 ASN cc_start: 0.7798 (t0) cc_final: 0.7518 (t0) REVERT: A 972 PHE cc_start: 0.8572 (t80) cc_final: 0.8333 (t80) REVERT: A 1087 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: A 1097 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8007 (ttp80) REVERT: A 1118 LYS cc_start: 0.6464 (tmtt) cc_final: 0.4703 (tmtt) REVERT: A 1185 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7376 (mtt-85) outliers start: 38 outliers final: 23 residues processed: 273 average time/residue: 0.2358 time to fit residues: 84.8761 Evaluate side-chains 278 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 74 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 374 GLN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114696 restraints weight = 13332.552| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.10 r_work: 0.3345 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8482 Z= 0.219 Angle : 0.618 13.914 11506 Z= 0.313 Chirality : 0.041 0.194 1380 Planarity : 0.004 0.049 1415 Dihedral : 6.073 132.610 1135 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.97 % Allowed : 24.42 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1039 helix: 1.40 (0.19), residues: 754 sheet: -0.08 (0.74), residues: 48 loop : -0.94 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 419 HIS 0.003 0.001 HIS A 614 PHE 0.032 0.001 PHE A 766 TYR 0.022 0.001 TYR A 267 ARG 0.013 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 2.005 Fit side-chains revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8314 (p) cc_final: 0.7977 (m) REVERT: A 154 MET cc_start: 0.8718 (mmm) cc_final: 0.8511 (mmm) REVERT: A 155 ASP cc_start: 0.7977 (t0) cc_final: 0.7632 (t0) REVERT: A 174 LEU cc_start: 0.8189 (tp) cc_final: 0.7964 (tp) REVERT: A 199 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7575 (mpp) REVERT: A 217 LEU cc_start: 0.8796 (mm) cc_final: 0.8531 (mm) REVERT: A 250 LYS cc_start: 0.8300 (mmmm) cc_final: 0.8020 (mttp) REVERT: A 258 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7191 (p) REVERT: A 295 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7750 (t0) REVERT: A 337 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6830 (tm-30) REVERT: A 383 MET cc_start: 0.6903 (mmm) cc_final: 0.6411 (mmm) REVERT: A 389 ILE cc_start: 0.8164 (mt) cc_final: 0.7906 (mm) REVERT: A 443 GLU cc_start: 0.7974 (tp30) cc_final: 0.7548 (tp30) REVERT: A 581 GLU cc_start: 0.7685 (tp30) cc_final: 0.7328 (tp30) REVERT: A 671 MET cc_start: 0.7419 (mtt) cc_final: 0.7159 (mtt) REVERT: A 678 MET cc_start: 0.6780 (tpp) cc_final: 0.6467 (mpp) REVERT: A 681 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 684 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8616 (tp) REVERT: A 746 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: A 810 MET cc_start: 0.5964 (tmm) cc_final: 0.5525 (tmm) REVERT: A 811 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5112 (pp) REVERT: A 822 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8409 (mt) REVERT: A 943 ASN cc_start: 0.7637 (t0) cc_final: 0.7272 (t0) REVERT: A 954 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 972 PHE cc_start: 0.8515 (t80) cc_final: 0.8285 (t80) REVERT: A 1008 LEU cc_start: 0.7881 (tt) cc_final: 0.7673 (tp) REVERT: A 1087 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: A 1097 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7951 (ttp80) REVERT: A 1116 LYS cc_start: 0.8120 (mtpm) cc_final: 0.7540 (mtpm) REVERT: A 1118 LYS cc_start: 0.6507 (tmtt) cc_final: 0.4727 (tmtt) REVERT: A 1185 ARG cc_start: 0.7592 (mtt-85) cc_final: 0.7374 (mtt-85) outliers start: 45 outliers final: 29 residues processed: 276 average time/residue: 0.2858 time to fit residues: 105.1714 Evaluate side-chains 289 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 702 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.132710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114436 restraints weight = 13262.534| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.09 r_work: 0.3338 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8482 Z= 0.235 Angle : 0.624 13.718 11506 Z= 0.316 Chirality : 0.041 0.197 1380 Planarity : 0.004 0.048 1415 Dihedral : 6.066 133.502 1135 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.53 % Allowed : 26.08 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1039 helix: 1.49 (0.19), residues: 754 sheet: -0.19 (0.72), residues: 48 loop : -0.89 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS A 350 PHE 0.021 0.001 PHE A 766 TYR 0.022 0.001 TYR A 267 ARG 0.014 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.989 Fit side-chains REVERT: A 78 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7613 (mt) REVERT: A 154 MET cc_start: 0.8700 (mmm) cc_final: 0.8264 (mtp) REVERT: A 155 ASP cc_start: 0.8052 (t0) cc_final: 0.7725 (t0) REVERT: A 174 LEU cc_start: 0.8210 (tp) cc_final: 0.7986 (tp) REVERT: A 199 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7357 (mmm) REVERT: A 217 LEU cc_start: 0.8772 (mm) cc_final: 0.8524 (mm) REVERT: A 250 LYS cc_start: 0.8319 (mmmm) cc_final: 0.8057 (mttp) REVERT: A 258 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7116 (p) REVERT: A 295 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7709 (t0) REVERT: A 337 GLU cc_start: 0.7580 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 383 MET cc_start: 0.7040 (mmm) cc_final: 0.6541 (mmm) REVERT: A 389 ILE cc_start: 0.8158 (mt) cc_final: 0.7902 (mm) REVERT: A 443 GLU cc_start: 0.7973 (tp30) cc_final: 0.7549 (tp30) REVERT: A 581 GLU cc_start: 0.7700 (tp30) cc_final: 0.7357 (tp30) REVERT: A 590 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 678 MET cc_start: 0.6753 (tpp) cc_final: 0.6449 (mpp) REVERT: A 681 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 684 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8625 (tp) REVERT: A 775 LEU cc_start: 0.8084 (mt) cc_final: 0.7707 (mt) REVERT: A 810 MET cc_start: 0.5895 (tmm) cc_final: 0.5406 (tmm) REVERT: A 811 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5126 (pp) REVERT: A 878 VAL cc_start: 0.8271 (t) cc_final: 0.8059 (t) REVERT: A 943 ASN cc_start: 0.7656 (t0) cc_final: 0.7327 (t0) REVERT: A 954 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 972 PHE cc_start: 0.8499 (t80) cc_final: 0.8290 (t80) REVERT: A 1008 LEU cc_start: 0.7959 (tt) cc_final: 0.7744 (tp) REVERT: A 1087 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: A 1097 ARG cc_start: 0.8332 (ttp80) cc_final: 0.7939 (ttp80) REVERT: A 1116 LYS cc_start: 0.8107 (mtpm) cc_final: 0.7487 (mtpm) REVERT: A 1118 LYS cc_start: 0.6576 (tmtt) cc_final: 0.4972 (mtmt) REVERT: A 1122 GLU cc_start: 0.8146 (tp30) cc_final: 0.7793 (tp30) outliers start: 41 outliers final: 29 residues processed: 266 average time/residue: 0.3029 time to fit residues: 106.7125 Evaluate side-chains 276 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114923 restraints weight = 13252.120| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.09 r_work: 0.3345 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8482 Z= 0.211 Angle : 0.620 13.781 11506 Z= 0.315 Chirality : 0.041 0.206 1380 Planarity : 0.004 0.050 1415 Dihedral : 6.013 132.411 1135 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.52 % Allowed : 25.41 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1039 helix: 1.59 (0.19), residues: 754 sheet: -0.24 (0.72), residues: 48 loop : -0.80 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.003 0.000 HIS A 350 PHE 0.040 0.002 PHE A 740 TYR 0.021 0.001 TYR A 267 ARG 0.013 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8686 (mmm) cc_final: 0.8272 (mtp) REVERT: A 155 ASP cc_start: 0.8066 (t0) cc_final: 0.7729 (t0) REVERT: A 174 LEU cc_start: 0.8212 (tp) cc_final: 0.8003 (tp) REVERT: A 217 LEU cc_start: 0.8745 (mm) cc_final: 0.8511 (mm) REVERT: A 250 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8092 (mttp) REVERT: A 258 THR cc_start: 0.7356 (OUTLIER) cc_final: 0.7080 (p) REVERT: A 295 ASN cc_start: 0.8074 (t0) cc_final: 0.7636 (t0) REVERT: A 337 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6841 (tm-30) REVERT: A 383 MET cc_start: 0.7049 (mmm) cc_final: 0.6534 (mmm) REVERT: A 389 ILE cc_start: 0.8161 (mt) cc_final: 0.7912 (mm) REVERT: A 443 GLU cc_start: 0.7969 (tp30) cc_final: 0.7535 (tp30) REVERT: A 581 GLU cc_start: 0.7682 (tp30) cc_final: 0.7375 (tp30) REVERT: A 606 GLU cc_start: 0.7727 (tp30) cc_final: 0.7415 (tp30) REVERT: A 678 MET cc_start: 0.6794 (tpp) cc_final: 0.6481 (mpp) REVERT: A 681 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 684 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 746 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: A 767 ASP cc_start: 0.7491 (m-30) cc_final: 0.7069 (p0) REVERT: A 810 MET cc_start: 0.5896 (tmm) cc_final: 0.5372 (tmm) REVERT: A 811 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5130 (pp) REVERT: A 943 ASN cc_start: 0.7617 (t0) cc_final: 0.7274 (t0) REVERT: A 954 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 1087 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: A 1113 THR cc_start: 0.8526 (t) cc_final: 0.8028 (p) REVERT: A 1116 LYS cc_start: 0.8096 (mtpm) cc_final: 0.7496 (mtpm) REVERT: A 1118 LYS cc_start: 0.6433 (tmtt) cc_final: 0.4884 (mtmt) REVERT: A 1122 GLU cc_start: 0.8115 (tp30) cc_final: 0.7770 (tp30) REVERT: A 1126 LEU cc_start: 0.8795 (mt) cc_final: 0.8557 (mp) REVERT: A 1185 ARG cc_start: 0.7521 (mtt-85) cc_final: 0.7201 (mtt-85) outliers start: 50 outliers final: 33 residues processed: 273 average time/residue: 0.2350 time to fit residues: 84.5954 Evaluate side-chains 279 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1137 ASN Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114330 restraints weight = 13311.658| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.09 r_work: 0.3340 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8482 Z= 0.222 Angle : 0.628 13.737 11506 Z= 0.318 Chirality : 0.041 0.188 1380 Planarity : 0.004 0.045 1415 Dihedral : 6.006 132.563 1135 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.41 % Allowed : 25.64 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1039 helix: 1.59 (0.19), residues: 759 sheet: -0.39 (0.71), residues: 48 loop : -0.69 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.003 0.001 HIS A 350 PHE 0.033 0.002 PHE A 740 TYR 0.021 0.001 TYR A 267 ARG 0.013 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7512 (mt) REVERT: A 116 VAL cc_start: 0.8383 (p) cc_final: 0.8167 (p) REVERT: A 154 MET cc_start: 0.8695 (mmm) cc_final: 0.8261 (mtp) REVERT: A 155 ASP cc_start: 0.8069 (t0) cc_final: 0.7742 (t0) REVERT: A 250 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8087 (mtmm) REVERT: A 258 THR cc_start: 0.7357 (OUTLIER) cc_final: 0.7081 (p) REVERT: A 295 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7748 (t0) REVERT: A 337 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6801 (tm-30) REVERT: A 383 MET cc_start: 0.7075 (mmm) cc_final: 0.6534 (mmm) REVERT: A 389 ILE cc_start: 0.8134 (mt) cc_final: 0.7880 (mm) REVERT: A 443 GLU cc_start: 0.7909 (tp30) cc_final: 0.7473 (tp30) REVERT: A 581 GLU cc_start: 0.7627 (tp30) cc_final: 0.7298 (tp30) REVERT: A 606 GLU cc_start: 0.7719 (tp30) cc_final: 0.7360 (tp30) REVERT: A 609 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: A 678 MET cc_start: 0.6797 (tpp) cc_final: 0.6494 (mpp) REVERT: A 681 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 684 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8648 (tp) REVERT: A 746 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: A 810 MET cc_start: 0.5935 (tmm) cc_final: 0.5430 (tmm) REVERT: A 811 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5142 (pp) REVERT: A 854 ILE cc_start: 0.8591 (tp) cc_final: 0.8347 (tt) REVERT: A 878 VAL cc_start: 0.8270 (t) cc_final: 0.8064 (t) REVERT: A 943 ASN cc_start: 0.7625 (t0) cc_final: 0.7285 (t0) REVERT: A 954 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7909 (mm-30) REVERT: A 1087 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: A 1113 THR cc_start: 0.8563 (t) cc_final: 0.8078 (p) REVERT: A 1116 LYS cc_start: 0.8152 (mtpm) cc_final: 0.7555 (mtpm) REVERT: A 1118 LYS cc_start: 0.6504 (tmtt) cc_final: 0.4990 (mtmt) REVERT: A 1122 GLU cc_start: 0.8124 (tp30) cc_final: 0.7752 (tp30) REVERT: A 1126 LEU cc_start: 0.8786 (mt) cc_final: 0.8546 (mp) REVERT: A 1185 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.7241 (mtt-85) outliers start: 49 outliers final: 33 residues processed: 266 average time/residue: 0.2321 time to fit residues: 81.2724 Evaluate side-chains 285 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A1156 HIS A1172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113903 restraints weight = 13351.269| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.10 r_work: 0.3334 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8482 Z= 0.235 Angle : 0.634 13.716 11506 Z= 0.322 Chirality : 0.041 0.170 1380 Planarity : 0.004 0.043 1415 Dihedral : 6.014 132.619 1135 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.08 % Allowed : 25.86 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1039 helix: 1.56 (0.19), residues: 760 sheet: -0.41 (0.71), residues: 48 loop : -0.76 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.015 0.001 HIS A1156 PHE 0.028 0.002 PHE A 740 TYR 0.022 0.001 TYR A 267 ARG 0.012 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7533 (mt) REVERT: A 116 VAL cc_start: 0.8386 (p) cc_final: 0.8173 (p) REVERT: A 154 MET cc_start: 0.8715 (mmm) cc_final: 0.8324 (mtp) REVERT: A 155 ASP cc_start: 0.8130 (t0) cc_final: 0.7773 (t0) REVERT: A 174 LEU cc_start: 0.8210 (tp) cc_final: 0.7978 (tp) REVERT: A 250 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8104 (mtmm) REVERT: A 258 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7077 (p) REVERT: A 295 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7733 (t0) REVERT: A 337 GLU cc_start: 0.7671 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 383 MET cc_start: 0.7141 (mmm) cc_final: 0.6596 (mmm) REVERT: A 389 ILE cc_start: 0.8146 (mt) cc_final: 0.7890 (mm) REVERT: A 443 GLU cc_start: 0.7912 (tp30) cc_final: 0.7476 (tp30) REVERT: A 581 GLU cc_start: 0.7719 (tp30) cc_final: 0.7401 (tp30) REVERT: A 606 GLU cc_start: 0.7705 (tp30) cc_final: 0.7351 (tp30) REVERT: A 609 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8054 (ttm-80) REVERT: A 678 MET cc_start: 0.6789 (tpp) cc_final: 0.6482 (mpp) REVERT: A 681 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 684 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8656 (tp) REVERT: A 746 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: A 767 ASP cc_start: 0.7522 (m-30) cc_final: 0.7123 (p0) REVERT: A 810 MET cc_start: 0.5930 (tmm) cc_final: 0.5418 (tmm) REVERT: A 811 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5124 (pp) REVERT: A 854 ILE cc_start: 0.8599 (tp) cc_final: 0.8377 (tt) REVERT: A 878 VAL cc_start: 0.8279 (t) cc_final: 0.8070 (t) REVERT: A 943 ASN cc_start: 0.7678 (t0) cc_final: 0.7349 (t0) REVERT: A 954 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 1060 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 1113 THR cc_start: 0.8573 (t) cc_final: 0.8073 (p) REVERT: A 1116 LYS cc_start: 0.8152 (mtpm) cc_final: 0.7542 (mtpm) REVERT: A 1118 LYS cc_start: 0.6499 (tmtt) cc_final: 0.4970 (mtmt) REVERT: A 1122 GLU cc_start: 0.8135 (tp30) cc_final: 0.7907 (tp30) REVERT: A 1126 LEU cc_start: 0.8798 (mt) cc_final: 0.8569 (mp) outliers start: 46 outliers final: 35 residues processed: 261 average time/residue: 0.2338 time to fit residues: 80.1662 Evaluate side-chains 283 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 101 optimal weight: 0.0270 chunk 21 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1156 HIS A1172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114763 restraints weight = 13487.984| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.11 r_work: 0.3342 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8482 Z= 0.204 Angle : 0.633 13.799 11506 Z= 0.319 Chirality : 0.041 0.160 1380 Planarity : 0.004 0.042 1415 Dihedral : 5.991 132.417 1135 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.08 % Allowed : 25.75 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1039 helix: 1.59 (0.19), residues: 764 sheet: -0.37 (0.72), residues: 48 loop : -0.95 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.023 0.001 HIS A1156 PHE 0.027 0.001 PHE A 766 TYR 0.021 0.001 TYR A 267 ARG 0.015 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7480 (mt) REVERT: A 116 VAL cc_start: 0.8375 (p) cc_final: 0.8153 (p) REVERT: A 154 MET cc_start: 0.8658 (mmm) cc_final: 0.8286 (mtp) REVERT: A 155 ASP cc_start: 0.8127 (t0) cc_final: 0.7767 (t0) REVERT: A 174 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7989 (tp) REVERT: A 250 LYS cc_start: 0.8366 (mmmm) cc_final: 0.8090 (mtmm) REVERT: A 258 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.7042 (p) REVERT: A 295 ASN cc_start: 0.8097 (t0) cc_final: 0.7719 (t0) REVERT: A 337 GLU cc_start: 0.7696 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 383 MET cc_start: 0.7086 (mmm) cc_final: 0.6547 (mmm) REVERT: A 389 ILE cc_start: 0.8157 (mt) cc_final: 0.7894 (mm) REVERT: A 443 GLU cc_start: 0.7906 (tp30) cc_final: 0.7493 (tp30) REVERT: A 581 GLU cc_start: 0.7703 (tp30) cc_final: 0.7367 (tp30) REVERT: A 606 GLU cc_start: 0.7701 (tp30) cc_final: 0.7382 (tp30) REVERT: A 609 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.8068 (ttm-80) REVERT: A 647 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7971 (mtmt) REVERT: A 678 MET cc_start: 0.6793 (tpp) cc_final: 0.6490 (mpp) REVERT: A 681 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 684 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8659 (tp) REVERT: A 746 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: A 767 ASP cc_start: 0.7472 (m-30) cc_final: 0.7072 (p0) REVERT: A 810 MET cc_start: 0.5905 (tmm) cc_final: 0.5384 (tmm) REVERT: A 811 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5111 (pp) REVERT: A 854 ILE cc_start: 0.8570 (tp) cc_final: 0.8340 (tt) REVERT: A 856 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7336 (ttm110) REVERT: A 878 VAL cc_start: 0.8263 (t) cc_final: 0.8063 (t) REVERT: A 943 ASN cc_start: 0.7615 (t0) cc_final: 0.7295 (t0) REVERT: A 954 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 1060 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 1113 THR cc_start: 0.8564 (t) cc_final: 0.8062 (p) REVERT: A 1116 LYS cc_start: 0.8156 (mtpm) cc_final: 0.7531 (mtpm) REVERT: A 1118 LYS cc_start: 0.6481 (tmtt) cc_final: 0.4957 (mtmt) REVERT: A 1122 GLU cc_start: 0.8120 (tp30) cc_final: 0.7892 (tp30) REVERT: A 1126 LEU cc_start: 0.8784 (mt) cc_final: 0.8547 (mp) REVERT: A 1151 THR cc_start: 0.7533 (m) cc_final: 0.6605 (m) outliers start: 46 outliers final: 36 residues processed: 258 average time/residue: 0.2438 time to fit residues: 82.7643 Evaluate side-chains 282 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.0170 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 HIS A1172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115131 restraints weight = 13408.491| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.11 r_work: 0.3359 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8482 Z= 0.202 Angle : 0.640 13.844 11506 Z= 0.323 Chirality : 0.041 0.163 1380 Planarity : 0.004 0.043 1415 Dihedral : 5.994 132.367 1135 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.19 % Allowed : 25.75 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1039 helix: 1.62 (0.19), residues: 764 sheet: -0.29 (0.72), residues: 48 loop : -0.85 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.020 0.001 HIS A1156 PHE 0.028 0.001 PHE A 766 TYR 0.021 0.001 TYR A 267 ARG 0.014 0.001 ARG A 733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7377 (mt) REVERT: A 116 VAL cc_start: 0.8378 (p) cc_final: 0.8156 (p) REVERT: A 154 MET cc_start: 0.8662 (mmm) cc_final: 0.8289 (mtp) REVERT: A 155 ASP cc_start: 0.8121 (t0) cc_final: 0.7772 (t0) REVERT: A 250 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8095 (mtmm) REVERT: A 258 THR cc_start: 0.7286 (OUTLIER) cc_final: 0.7000 (p) REVERT: A 295 ASN cc_start: 0.8115 (t0) cc_final: 0.7748 (t0) REVERT: A 337 GLU cc_start: 0.7700 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 383 MET cc_start: 0.7075 (mmm) cc_final: 0.6546 (mmm) REVERT: A 389 ILE cc_start: 0.8157 (mt) cc_final: 0.7897 (mm) REVERT: A 443 GLU cc_start: 0.7908 (tp30) cc_final: 0.7497 (tp30) REVERT: A 581 GLU cc_start: 0.7679 (tp30) cc_final: 0.7299 (tp30) REVERT: A 606 GLU cc_start: 0.7696 (tp30) cc_final: 0.7338 (tp30) REVERT: A 609 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8039 (ttm-80) REVERT: A 647 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7966 (mtmt) REVERT: A 678 MET cc_start: 0.6773 (tpp) cc_final: 0.6469 (mpp) REVERT: A 681 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7514 (tm-30) REVERT: A 684 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8632 (tp) REVERT: A 746 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: A 767 ASP cc_start: 0.7469 (m-30) cc_final: 0.7065 (p0) REVERT: A 810 MET cc_start: 0.5903 (tmm) cc_final: 0.5382 (tmm) REVERT: A 811 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5107 (pp) REVERT: A 854 ILE cc_start: 0.8552 (tp) cc_final: 0.8345 (tt) REVERT: A 856 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7294 (ttm110) REVERT: A 943 ASN cc_start: 0.7606 (t0) cc_final: 0.7335 (t0) REVERT: A 954 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 1060 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 1113 THR cc_start: 0.8569 (t) cc_final: 0.8068 (p) REVERT: A 1116 LYS cc_start: 0.8139 (mtpm) cc_final: 0.7516 (mtpm) REVERT: A 1118 LYS cc_start: 0.6489 (tmtt) cc_final: 0.4957 (mtmt) REVERT: A 1122 GLU cc_start: 0.8113 (tp30) cc_final: 0.7885 (tp30) REVERT: A 1126 LEU cc_start: 0.8772 (mt) cc_final: 0.8531 (mp) REVERT: A 1172 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.6342 (m90) outliers start: 47 outliers final: 37 residues processed: 262 average time/residue: 0.2356 time to fit residues: 81.2014 Evaluate side-chains 283 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.0000 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 0.0010 chunk 22 optimal weight: 0.3980 chunk 104 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A1156 HIS A1172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116144 restraints weight = 13359.344| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.12 r_work: 0.3375 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8482 Z= 0.185 Angle : 0.633 13.820 11506 Z= 0.318 Chirality : 0.040 0.169 1380 Planarity : 0.004 0.056 1415 Dihedral : 5.975 132.237 1135 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.53 % Allowed : 26.30 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1039 helix: 1.67 (0.19), residues: 764 sheet: -0.22 (0.73), residues: 48 loop : -0.81 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 763 HIS 0.018 0.001 HIS A1156 PHE 0.029 0.001 PHE A 766 TYR 0.020 0.001 TYR A 267 ARG 0.013 0.001 ARG A 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5198.57 seconds wall clock time: 91 minutes 39.18 seconds (5499.18 seconds total)