Starting phenix.real_space_refine on Wed Aug 5 03:13:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq8_38569/08_2026/8xq8_38569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq8_38569/08_2026/8xq8_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_38569/08_2026/8xq8_38569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq8_38569/08_2026/8xq8_38569.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq8_38569/08_2026/8xq8_38569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq8_38569/08_2026/8xq8_38569.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 1.37, per 1000 atoms: 0.16 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: 0.61 Conformation dependent library (CDL) restraints added in 263.1 milliseconds 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: 0.25 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: 1.29 Time building geometry restraints manager: 0.83 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: 11289 3.81 - 7.63: 174 7.63 - 11.44: 35 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 - 17.80: 4330 17.80 - 35.59: 561 35.59 - 53.39: 143 53.39 - 71.19: 25 71.19 - 88.98: 14 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: 1147 0.073 - 0.145: 186 0.145 - 0.218: 38 0.218 - 0.290: 5 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: 0.920 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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= 0.311 Angle : 1.256 19.067 11506 Z= 0.647 Chirality : 0.061 0.363 1380 Planarity : 0.010 0.158 1415 Dihedral : 17.386 88.983 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.018 0.002 ARG A1123 TYR 0.045 0.002 TYR A 267 PHE 0.092 0.003 PHE A 766 TRP 0.016 0.002 TRP A 427 HIS 0.024 0.002 HIS A1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.31 ( 8482) covalent geometry : angle 1.25602 / 0.65 (11506) hydrogen bonds : bond 0.11763 / 7.69 ( 616) hydrogen bonds : angle 6.25932 / 4.49 ( 1833) *********************** 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 : 0.266 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: 0.7822 (tp) REVERT: A 263 GLN cc_start: 0.7713 (mt0) cc_final: 0.7116 (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: 0.7631 (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: 0.7299 (OUTLIER) cc_final: 0.7020 (pt) outliers start: 7 outliers final: 3 residues processed: 260 average time/residue: 0.0776 time to fit residues: 27.3641 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 : 0.273 ------------------------------------------------------------------------------- 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 49 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.9007 > 50:) chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN A 292 HIS A 295 ASN A 444 ASN A 624 GLN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A 955 ASN ** A1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3738 r_free = 0.3738 target = 0.133516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114902 restraints weight = 13380.627| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.08 r_work: 0.3340 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1475 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= 0.194 Angle : 0.694 14.324 11506 Z= 0.348 Chirality : 0.043 0.220 1380 Planarity : 0.005 0.059 1415 Dihedral : 4.858 35.627 1139 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.53 % Allowed : 23.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1039 helix: 0.69 (0.18), residues: 754 sheet: -0.37 (0.69), residues: 48 loop : -0.93 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 733 TYR 0.019 0.002 TYR A 267 PHE 0.031 0.002 PHE A 766 TRP 0.011 0.001 TRP A 193 HIS 0.005 0.001 HIS A1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 8482) covalent geometry : angle 0.69376 / 0.35 (11506) hydrogen bonds : bond 0.05427 / 3.62 ( 616) hydrogen bonds : angle 4.81732 / 3.48 ( 1833) *********************** 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 297 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.228 Fit side-chains REVERT: A 116 VAL cc_start: 0.8353 (p) cc_final: 0.8009 (m) REVERT: A 155 ASP cc_start: 0.7889 (t0) cc_final: 0.7635 (t0) REVERT: A 174 LEU cc_start: 0.8145 (tp) cc_final: 0.7698 (tp) REVERT: A 179 VAL cc_start: 0.8066 (t) cc_final: 0.7579 (p) REVERT: A 250 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7736 (mttp) REVERT: A 258 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7256 (p) REVERT: A 295 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7567 (t0) REVERT: A 337 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7129 (tm-30) REVERT: A 381 ASP cc_start: 0.7437 (m-30) cc_final: 0.7188 (m-30) REVERT: A 383 MET cc_start: 0.6617 (mmm) cc_final: 0.6282 (mmm) REVERT: A 389 ILE cc_start: 0.8198 (mt) cc_final: 0.7940 (mm) REVERT: A 443 GLU cc_start: 0.7991 (tp30) cc_final: 0.7553 (tp30) REVERT: A 671 MET cc_start: 0.7247 (mtt) cc_final: 0.6962 (mtt) REVERT: A 678 MET cc_start: 0.6720 (tpp) cc_final: 0.6419 (mpp) REVERT: A 681 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 684 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 810 MET cc_start: 0.5887 (tmm) cc_final: 0.5647 (tmm) REVERT: A 853 ILE cc_start: 0.8806 (tt) cc_final: 0.8415 (tp) REVERT: A 943 ASN cc_start: 0.7648 (t0) cc_final: 0.7330 (t0) REVERT: A 969 LEU cc_start: 0.8699 (tp) cc_final: 0.8440 (tp) REVERT: A 972 PHE cc_start: 0.8545 (t80) cc_final: 0.8330 (t80) REVERT: A 1087 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: A 1097 ARG cc_start: 0.8432 (ttp80) cc_final: 0.7922 (ttp80) REVERT: A 1118 LYS cc_start: 0.6296 (tmtt) cc_final: 0.5447 (tmtt) REVERT: A 1123 ARG cc_start: 0.8309 (mtp-110) cc_final: 0.7071 (mmp-170) outliers start: 41 outliers final: 18 residues processed: 277 average time/residue: 0.0758 time to fit residues: 28.3548 Evaluate side-chains 262 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL 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 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 419 TRP 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 814 THR 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 1002 VAL 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 18 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 102 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN A 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 ASN A1114 GLN A1135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.134902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116292 restraints weight = 13400.909| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.11 r_work: 0.3361 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8482 Z= 0.145 Angle : 0.640 13.571 11506 Z= 0.318 Chirality : 0.041 0.198 1380 Planarity : 0.004 0.058 1415 Dihedral : 4.613 35.852 1135 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.42 % Allowed : 24.64 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1039 helix: 1.23 (0.19), residues: 751 sheet: -0.10 (0.72), residues: 48 loop : -0.99 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 733 TYR 0.020 0.001 TYR A 267 PHE 0.023 0.001 PHE A 766 TRP 0.007 0.001 TRP A 635 HIS 0.003 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 8482) covalent geometry : angle 0.63980 / 0.32 (11506) hydrogen bonds : bond 0.04863 / 3.24 ( 616) hydrogen bonds : angle 4.66033 / 3.35 ( 1833) *********************** 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 286 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.239 Fit side-chains REVERT: A 155 ASP cc_start: 0.7883 (t0) cc_final: 0.7563 (t0) REVERT: A 174 LEU cc_start: 0.8178 (tp) cc_final: 0.7866 (tp) REVERT: A 250 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7920 (mttp) REVERT: A 258 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7164 (p) REVERT: A 295 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7724 (t0) REVERT: A 337 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7039 (tm-30) REVERT: A 359 LEU cc_start: 0.8763 (mt) cc_final: 0.8432 (mp) REVERT: A 383 MET cc_start: 0.6630 (mmm) cc_final: 0.6271 (mmm) REVERT: A 389 ILE cc_start: 0.8201 (mt) cc_final: 0.7943 (mm) REVERT: A 443 GLU cc_start: 0.7975 (tp30) cc_final: 0.7542 (tp30) REVERT: A 671 MET cc_start: 0.7320 (mtt) cc_final: 0.7109 (mtt) REVERT: A 678 MET cc_start: 0.6699 (tpp) cc_final: 0.6393 (mpp) REVERT: A 681 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 684 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8604 (tp) REVERT: A 810 MET cc_start: 0.5964 (tmm) cc_final: 0.5598 (tmm) REVERT: A 822 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 853 ILE cc_start: 0.8845 (tt) cc_final: 0.8450 (tp) REVERT: A 943 ASN cc_start: 0.7491 (t0) cc_final: 0.7169 (t0) REVERT: A 954 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7946 (mm-30) REVERT: A 972 PHE cc_start: 0.8495 (t80) cc_final: 0.8259 (t80) REVERT: A 1008 LEU cc_start: 0.7885 (tt) cc_final: 0.7639 (tp) REVERT: A 1086 LEU cc_start: 0.8371 (mt) cc_final: 0.8165 (mt) REVERT: A 1087 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: A 1097 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7952 (ttp80) REVERT: A 1116 LYS cc_start: 0.8112 (mtpm) cc_final: 0.7471 (mtpm) REVERT: A 1118 LYS cc_start: 0.6250 (tmtt) cc_final: 0.5177 (tmtt) REVERT: A 1190 ARG cc_start: 0.7328 (mpt180) cc_final: 0.7113 (mpt180) outliers start: 40 outliers final: 19 residues processed: 263 average time/residue: 0.0782 time to fit residues: 27.4991 Evaluate side-chains 265 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 251 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 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 822 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1047 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 Chi-restraints excluded: chain A residue 1105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 44 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN A 444 ASN A 502 HIS A 677 HIS ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116490 restraints weight = 13557.826| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.12 r_work: 0.3373 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2073 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= 0.142 Angle : 0.623 13.778 11506 Z= 0.309 Chirality : 0.041 0.179 1380 Planarity : 0.004 0.045 1415 Dihedral : 4.495 35.675 1135 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.31 % Allowed : 25.19 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1039 helix: 1.50 (0.19), residues: 751 sheet: -0.06 (0.73), residues: 48 loop : -0.91 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 733 TYR 0.020 0.001 TYR A 267 PHE 0.021 0.001 PHE A 766 TRP 0.007 0.001 TRP A 353 HIS 0.008 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8482) covalent geometry : angle 0.62333 / 0.31 (11506) hydrogen bonds : bond 0.04739 / 3.16 ( 616) hydrogen bonds : angle 4.55536 / 3.27 ( 1833) *********************** 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 282 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 0.185 Fit side-chains REVERT: A 116 VAL cc_start: 0.8283 (p) cc_final: 0.7974 (m) REVERT: A 155 ASP cc_start: 0.7908 (t0) cc_final: 0.7550 (t0) REVERT: A 174 LEU cc_start: 0.8188 (tp) cc_final: 0.7907 (tp) REVERT: A 217 LEU cc_start: 0.8767 (mm) cc_final: 0.8527 (mm) REVERT: A 250 LYS cc_start: 0.8275 (mmmm) cc_final: 0.8008 (mttp) REVERT: A 258 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7094 (p) REVERT: A 295 ASN cc_start: 0.8065 (t160) cc_final: 0.7808 (t0) REVERT: A 337 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6976 (tm-30) REVERT: A 383 MET cc_start: 0.6678 (mmm) cc_final: 0.6236 (mmm) REVERT: A 389 ILE cc_start: 0.8149 (mt) cc_final: 0.7883 (mm) REVERT: A 443 GLU cc_start: 0.7980 (tp30) cc_final: 0.7557 (tp30) REVERT: A 647 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8069 (mmtm) REVERT: A 678 MET cc_start: 0.6707 (tpp) cc_final: 0.6411 (mpp) REVERT: A 681 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 684 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8607 (tp) REVERT: A 746 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: A 763 TRP cc_start: 0.6951 (m-90) cc_final: 0.6643 (m100) REVERT: A 810 MET cc_start: 0.5998 (tmm) cc_final: 0.5552 (tmm) REVERT: A 811 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5094 (pp) REVERT: A 822 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8392 (mt) REVERT: A 853 ILE cc_start: 0.8890 (tt) cc_final: 0.8635 (tt) REVERT: A 888 GLU cc_start: 0.8037 (tp30) cc_final: 0.7826 (tp30) REVERT: A 943 ASN cc_start: 0.7532 (t0) cc_final: 0.7157 (t0) REVERT: A 954 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 968 LYS cc_start: 0.8262 (ttmm) cc_final: 0.8043 (ttmm) REVERT: A 972 PHE cc_start: 0.8507 (t80) cc_final: 0.8299 (t80) REVERT: A 1008 LEU cc_start: 0.7829 (tt) cc_final: 0.7581 (tp) REVERT: A 1087 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: A 1097 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7941 (ttp80) REVERT: A 1113 THR cc_start: 0.8479 (t) cc_final: 0.7942 (p) REVERT: A 1116 LYS cc_start: 0.8110 (mtpm) cc_final: 0.7487 (mtpm) REVERT: A 1118 LYS cc_start: 0.6538 (tmtt) cc_final: 0.5178 (mtmt) REVERT: A 1190 ARG cc_start: 0.7345 (mpt180) cc_final: 0.7050 (mpt180) outliers start: 39 outliers final: 23 residues processed: 258 average time/residue: 0.0787 time to fit residues: 27.1088 Evaluate side-chains 266 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 647 LYS 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 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 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1047 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 Chi-restraints excluded: chain A residue 1105 GLU 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 89 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 502 HIS ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 ASN A1137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115462 restraints weight = 13365.221| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.11 r_work: 0.3356 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8482 Z= 0.164 Angle : 0.636 13.547 11506 Z= 0.315 Chirality : 0.042 0.205 1380 Planarity : 0.004 0.047 1415 Dihedral : 4.461 35.027 1135 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.75 % Allowed : 25.08 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1039 helix: 1.53 (0.19), residues: 755 sheet: -0.13 (0.74), residues: 48 loop : -0.86 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 733 TYR 0.021 0.001 TYR A 267 PHE 0.033 0.001 PHE A 766 TRP 0.012 0.001 TRP A 763 HIS 0.006 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 8482) covalent geometry : angle 0.63624 / 0.31 (11506) hydrogen bonds : bond 0.04962 / 3.31 ( 616) hydrogen bonds : angle 4.53988 / 3.25 ( 1833) *********************** 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 294 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.200 Fit side-chains REVERT: A 155 ASP cc_start: 0.8014 (t0) cc_final: 0.7631 (t0) REVERT: A 174 LEU cc_start: 0.8220 (tp) cc_final: 0.7987 (tp) REVERT: A 199 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7405 (mmm) REVERT: A 217 LEU cc_start: 0.8783 (mm) cc_final: 0.8520 (mm) REVERT: A 250 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8036 (mttp) REVERT: A 258 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7086 (p) REVERT: A 295 ASN cc_start: 0.8157 (t160) cc_final: 0.7811 (t0) REVERT: A 337 GLU cc_start: 0.7646 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 380 VAL cc_start: 0.8220 (m) cc_final: 0.7893 (t) REVERT: A 383 MET cc_start: 0.6840 (mmm) cc_final: 0.6398 (mmm) REVERT: A 389 ILE cc_start: 0.8164 (mt) cc_final: 0.7904 (mm) REVERT: A 443 GLU cc_start: 0.7968 (tp30) cc_final: 0.7543 (tp30) REVERT: A 581 GLU cc_start: 0.7702 (tp30) cc_final: 0.7339 (tp30) REVERT: A 606 GLU cc_start: 0.7730 (tp30) cc_final: 0.7500 (tp30) REVERT: A 678 MET cc_start: 0.6772 (tpp) cc_final: 0.6457 (mpp) REVERT: A 681 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 684 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 746 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: A 810 MET cc_start: 0.6030 (tmm) cc_final: 0.5589 (tmm) REVERT: A 811 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5237 (pp) REVERT: A 815 LYS cc_start: 0.8549 (tppp) cc_final: 0.8309 (tppp) REVERT: A 853 ILE cc_start: 0.8963 (tt) cc_final: 0.8729 (tt) REVERT: A 943 ASN cc_start: 0.7641 (t0) cc_final: 0.7309 (t0) REVERT: A 954 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 968 LYS cc_start: 0.8267 (ttmm) cc_final: 0.8043 (ttmm) REVERT: A 972 PHE cc_start: 0.8489 (t80) cc_final: 0.8272 (t80) REVERT: A 1087 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: A 1097 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7920 (ttp80) REVERT: A 1113 THR cc_start: 0.8520 (t) cc_final: 0.7960 (p) REVERT: A 1116 LYS cc_start: 0.8120 (mtpm) cc_final: 0.7503 (mtpm) REVERT: A 1118 LYS cc_start: 0.6498 (tmtt) cc_final: 0.4911 (mtmt) REVERT: A 1122 GLU cc_start: 0.8172 (tp30) cc_final: 0.7713 (tp30) REVERT: A 1190 ARG cc_start: 0.7287 (mpt180) cc_final: 0.6877 (mpt180) outliers start: 43 outliers final: 26 residues processed: 266 average time/residue: 0.0758 time to fit residues: 26.8362 Evaluate side-chains 278 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 251 MET 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 689 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 746 GLU 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 838 ASP Chi-restraints excluded: chain A residue 864 LEU 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 994 GLU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1047 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 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 40 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 96 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115593 restraints weight = 13197.539| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.08 r_work: 0.3347 rms_B_bonded: 2.58 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: 0.7780 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8482 Z= 0.152 Angle : 0.634 13.685 11506 Z= 0.313 Chirality : 0.041 0.198 1380 Planarity : 0.004 0.054 1415 Dihedral : 4.417 34.547 1135 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.75 % Allowed : 25.41 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.26), residues: 1039 helix: 1.58 (0.19), residues: 756 sheet: -0.22 (0.75), residues: 48 loop : -0.80 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 733 TYR 0.021 0.001 TYR A 267 PHE 0.031 0.001 PHE A 766 TRP 0.031 0.001 TRP A 763 HIS 0.006 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 8482) covalent geometry : angle 0.63402 / 0.31 (11506) hydrogen bonds : bond 0.04811 / 3.23 ( 616) hydrogen bonds : angle 4.47205 / 3.20 ( 1833) *********************** 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 292 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.252 Fit side-chains REVERT: A 77 VAL cc_start: 0.8073 (p) cc_final: 0.7826 (t) REVERT: A 116 VAL cc_start: 0.8403 (p) cc_final: 0.8160 (p) REVERT: A 155 ASP cc_start: 0.8044 (t0) cc_final: 0.7665 (t0) REVERT: A 174 LEU cc_start: 0.8233 (tp) cc_final: 0.8012 (tp) REVERT: A 195 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7199 (t80) REVERT: A 199 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7509 (mpp) REVERT: A 250 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7958 (mtmm) REVERT: A 258 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7040 (p) REVERT: A 295 ASN cc_start: 0.8187 (t160) cc_final: 0.7776 (t0) REVERT: A 337 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6905 (tm-30) REVERT: A 380 VAL cc_start: 0.8239 (m) cc_final: 0.7925 (t) REVERT: A 383 MET cc_start: 0.6863 (mmm) cc_final: 0.6422 (mmm) REVERT: A 389 ILE cc_start: 0.8147 (mt) cc_final: 0.7888 (mm) REVERT: A 443 GLU cc_start: 0.7924 (tp30) cc_final: 0.7496 (tp30) REVERT: A 581 GLU cc_start: 0.7627 (tp30) cc_final: 0.7322 (tp30) REVERT: A 606 GLU cc_start: 0.7743 (tp30) cc_final: 0.7500 (tp30) REVERT: A 678 MET cc_start: 0.6782 (tpp) cc_final: 0.6497 (mpp) REVERT: A 681 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 684 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8626 (tp) REVERT: A 767 ASP cc_start: 0.7582 (m-30) cc_final: 0.7161 (p0) REVERT: A 810 MET cc_start: 0.6018 (tmm) cc_final: 0.5575 (tmm) REVERT: A 811 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5200 (pp) REVERT: A 943 ASN cc_start: 0.7617 (t0) cc_final: 0.7382 (t0) REVERT: A 1087 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: A 1113 THR cc_start: 0.8532 (t) cc_final: 0.7993 (p) REVERT: A 1116 LYS cc_start: 0.8135 (mtpm) cc_final: 0.7532 (mtpm) REVERT: A 1118 LYS cc_start: 0.6576 (tmtt) cc_final: 0.5003 (mtmt) REVERT: A 1122 GLU cc_start: 0.8179 (tp30) cc_final: 0.7745 (tp30) REVERT: A 1126 LEU cc_start: 0.8626 (mt) cc_final: 0.8366 (mp) REVERT: A 1190 ARG cc_start: 0.7199 (mpt180) cc_final: 0.6689 (mpt180) outliers start: 43 outliers final: 28 residues processed: 267 average time/residue: 0.0718 time to fit residues: 25.9541 Evaluate side-chains 281 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 251 MET 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 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 697 MET 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 837 TYR Chi-restraints excluded: chain A residue 838 ASP 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 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 1146 ILE Chi-restraints excluded: chain A residue 1149 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114393 restraints weight = 13406.347| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.10 r_work: 0.3332 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8482 Z= 0.163 Angle : 0.637 13.661 11506 Z= 0.317 Chirality : 0.041 0.188 1380 Planarity : 0.004 0.056 1415 Dihedral : 4.428 34.153 1135 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.52 % Allowed : 24.75 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1039 helix: 1.60 (0.19), residues: 758 sheet: -0.25 (0.72), residues: 48 loop : -0.67 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 733 TYR 0.021 0.001 TYR A 267 PHE 0.027 0.001 PHE A 766 TRP 0.021 0.001 TRP A 763 HIS 0.014 0.001 HIS A1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 8482) covalent geometry : angle 0.63699 / 0.32 (11506) hydrogen bonds : bond 0.04896 / 3.28 ( 616) hydrogen bonds : angle 4.48322 / 3.21 ( 1833) *********************** 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 302 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.174 Fit side-chains REVERT: A 78 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7454 (mt) REVERT: A 116 VAL cc_start: 0.8401 (p) cc_final: 0.8165 (p) REVERT: A 155 ASP cc_start: 0.8057 (t0) cc_final: 0.7683 (t0) REVERT: A 195 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.7256 (t80) REVERT: A 199 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7528 (mpp) REVERT: A 214 VAL cc_start: 0.8287 (m) cc_final: 0.8085 (p) REVERT: A 250 LYS cc_start: 0.8333 (mmmm) cc_final: 0.8020 (mtmm) REVERT: A 258 THR cc_start: 0.7338 (OUTLIER) cc_final: 0.7053 (p) REVERT: A 295 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7770 (t0) REVERT: A 337 GLU cc_start: 0.7658 (tm-30) cc_final: 0.6841 (tm-30) REVERT: A 380 VAL cc_start: 0.8292 (m) cc_final: 0.7990 (t) REVERT: A 383 MET cc_start: 0.6949 (mmm) cc_final: 0.6463 (mmm) REVERT: A 389 ILE cc_start: 0.8153 (mt) cc_final: 0.7894 (mm) REVERT: A 443 GLU cc_start: 0.7933 (tp30) cc_final: 0.7497 (tp30) REVERT: A 581 GLU cc_start: 0.7626 (tp30) cc_final: 0.7307 (tp30) REVERT: A 606 GLU cc_start: 0.7722 (tp30) cc_final: 0.7360 (tp30) REVERT: A 678 MET cc_start: 0.6817 (tpp) cc_final: 0.6546 (mpp) REVERT: A 681 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 684 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 746 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: A 810 MET cc_start: 0.6037 (tmm) cc_final: 0.5583 (tmm) REVERT: A 811 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5232 (pp) REVERT: A 943 ASN cc_start: 0.7673 (t0) cc_final: 0.7448 (t0) REVERT: A 1087 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: A 1113 THR cc_start: 0.8550 (t) cc_final: 0.8004 (p) REVERT: A 1116 LYS cc_start: 0.8150 (mtpm) cc_final: 0.7545 (mtpm) REVERT: A 1118 LYS cc_start: 0.6485 (tmtt) cc_final: 0.4924 (mtmt) REVERT: A 1122 GLU cc_start: 0.8134 (tp30) cc_final: 0.7727 (tp30) REVERT: A 1126 LEU cc_start: 0.8671 (mt) cc_final: 0.8451 (mp) REVERT: A 1185 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.7244 (mtp85) REVERT: A 1190 ARG cc_start: 0.7180 (mpt180) cc_final: 0.6807 (mpt180) outliers start: 50 outliers final: 33 residues processed: 270 average time/residue: 0.0779 time to fit residues: 28.0961 Evaluate side-chains 285 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 195 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 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 483 MET Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET 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 697 MET Chi-restraints excluded: chain A residue 746 GLU 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 837 TYR 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 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1047 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 Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1137 ASN Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 84 optimal weight: 0.0470 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 691 ASN A1137 ASN A1172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115057 restraints weight = 13337.256| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.08 r_work: 0.3356 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8482 Z= 0.160 Angle : 0.649 13.674 11506 Z= 0.325 Chirality : 0.041 0.187 1380 Planarity : 0.004 0.063 1415 Dihedral : 4.450 33.877 1135 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.86 % Allowed : 24.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1039 helix: 1.59 (0.19), residues: 760 sheet: -0.42 (0.71), residues: 48 loop : -0.62 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1123 TYR 0.021 0.001 TYR A 267 PHE 0.047 0.002 PHE A 740 TRP 0.024 0.002 TRP A 763 HIS 0.009 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 8482) covalent geometry : angle 0.64909 / 0.33 (11506) hydrogen bonds : bond 0.04862 / 3.27 ( 616) hydrogen bonds : angle 4.46829 / 3.20 ( 1833) *********************** 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 305 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 0.256 Fit side-chains REVERT: A 78 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 116 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8151 (p) REVERT: A 174 LEU cc_start: 0.8222 (tp) cc_final: 0.7991 (tp) REVERT: A 195 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7282 (t80) REVERT: A 199 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7568 (mpp) REVERT: A 214 VAL cc_start: 0.8259 (m) cc_final: 0.8049 (p) REVERT: A 250 LYS cc_start: 0.8327 (mmmm) cc_final: 0.8022 (mtmm) REVERT: A 258 THR cc_start: 0.7319 (OUTLIER) cc_final: 0.7036 (p) REVERT: A 295 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7787 (t0) REVERT: A 337 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 359 LEU cc_start: 0.8741 (mt) cc_final: 0.8411 (mp) REVERT: A 380 VAL cc_start: 0.8303 (m) cc_final: 0.8016 (t) REVERT: A 383 MET cc_start: 0.6975 (mmm) cc_final: 0.6474 (mmm) REVERT: A 389 ILE cc_start: 0.8158 (mt) cc_final: 0.7899 (mm) REVERT: A 443 GLU cc_start: 0.7918 (tp30) cc_final: 0.7564 (tp30) REVERT: A 581 GLU cc_start: 0.7693 (tp30) cc_final: 0.7371 (tp30) REVERT: A 606 GLU cc_start: 0.7698 (tp30) cc_final: 0.7338 (tp30) REVERT: A 678 MET cc_start: 0.6773 (tpp) cc_final: 0.6513 (mpp) REVERT: A 681 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7509 (tm-30) REVERT: A 684 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8639 (tp) REVERT: A 746 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: A 767 ASP cc_start: 0.7506 (m-30) cc_final: 0.7304 (p0) REVERT: A 800 LYS cc_start: 0.8358 (pttt) cc_final: 0.8095 (pptt) REVERT: A 810 MET cc_start: 0.6080 (tmm) cc_final: 0.5604 (tmm) REVERT: A 811 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5224 (pp) REVERT: A 854 ILE cc_start: 0.8666 (tp) cc_final: 0.8426 (tt) REVERT: A 943 ASN cc_start: 0.7681 (t0) cc_final: 0.7449 (t0) REVERT: A 1060 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 1087 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: A 1113 THR cc_start: 0.8555 (t) cc_final: 0.8031 (p) REVERT: A 1116 LYS cc_start: 0.8145 (mtpm) cc_final: 0.7533 (mtpm) REVERT: A 1118 LYS cc_start: 0.6494 (tmtt) cc_final: 0.4943 (mtmt) REVERT: A 1122 GLU cc_start: 0.8100 (tp30) cc_final: 0.7723 (tp30) REVERT: A 1126 LEU cc_start: 0.8650 (mt) cc_final: 0.8423 (mp) REVERT: A 1190 ARG cc_start: 0.7143 (mpt180) cc_final: 0.6758 (mpt180) outliers start: 53 outliers final: 36 residues processed: 272 average time/residue: 0.0806 time to fit residues: 29.3905 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 : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 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 483 MET Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET 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 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 837 TYR 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 987 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1047 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 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 1172 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN A1172 HIS 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 = 0.132605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.114402 restraints weight = 13320.765| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.06 r_work: 0.3334 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8482 Z= 0.177 Angle : 0.664 13.678 11506 Z= 0.333 Chirality : 0.042 0.186 1380 Planarity : 0.005 0.063 1415 Dihedral : 4.471 33.409 1135 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.52 % Allowed : 25.97 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.26), residues: 1039 helix: 1.58 (0.19), residues: 760 sheet: -0.08 (0.80), residues: 38 loop : -0.60 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1123 TYR 0.020 0.001 TYR A 267 PHE 0.044 0.002 PHE A 740 TRP 0.023 0.002 TRP A 763 HIS 0.008 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 8482) covalent geometry : angle 0.66444 / 0.33 (11506) hydrogen bonds : bond 0.04997 / 3.36 ( 616) hydrogen bonds : angle 4.51105 / 3.22 ( 1833) *********************** 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 299 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 0.309 Fit side-chains REVERT: A 78 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7547 (mt) REVERT: A 116 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8160 (p) REVERT: A 174 LEU cc_start: 0.8208 (tp) cc_final: 0.7984 (tp) REVERT: A 195 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 199 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7571 (mpp) REVERT: A 228 THR cc_start: 0.8432 (m) cc_final: 0.8206 (t) REVERT: A 250 LYS cc_start: 0.8358 (mmmm) cc_final: 0.8051 (mtmm) REVERT: A 258 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.7008 (p) REVERT: A 295 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7794 (t0) REVERT: A 337 GLU cc_start: 0.7683 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 359 LEU cc_start: 0.8730 (mt) cc_final: 0.8405 (mp) REVERT: A 380 VAL cc_start: 0.8319 (m) cc_final: 0.8036 (t) REVERT: A 383 MET cc_start: 0.7004 (mmm) cc_final: 0.6510 (mmm) REVERT: A 389 ILE cc_start: 0.8169 (mt) cc_final: 0.7900 (mm) REVERT: A 404 SER cc_start: 0.8366 (p) cc_final: 0.8137 (p) REVERT: A 581 GLU cc_start: 0.7702 (tp30) cc_final: 0.7356 (tp30) REVERT: A 606 GLU cc_start: 0.7702 (tp30) cc_final: 0.7359 (tp30) REVERT: A 678 MET cc_start: 0.6778 (tpp) cc_final: 0.6535 (mpp) REVERT: A 681 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 684 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8653 (tp) REVERT: A 746 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: A 767 ASP cc_start: 0.7513 (m-30) cc_final: 0.7144 (p0) REVERT: A 800 LYS cc_start: 0.8376 (pttt) cc_final: 0.8138 (pptt) REVERT: A 810 MET cc_start: 0.6092 (tmm) cc_final: 0.5602 (tmm) REVERT: A 811 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5203 (pp) REVERT: A 854 ILE cc_start: 0.8680 (tp) cc_final: 0.8424 (tt) REVERT: A 943 ASN cc_start: 0.7719 (t0) cc_final: 0.7510 (t0) REVERT: A 1060 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 1087 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: A 1113 THR cc_start: 0.8561 (t) cc_final: 0.8069 (p) REVERT: A 1116 LYS cc_start: 0.8148 (mtpm) cc_final: 0.7543 (mtpm) REVERT: A 1118 LYS cc_start: 0.6550 (tmtt) cc_final: 0.4990 (mtmt) REVERT: A 1122 GLU cc_start: 0.8122 (tp30) cc_final: 0.7744 (tp30) REVERT: A 1126 LEU cc_start: 0.8683 (mt) cc_final: 0.8471 (mp) REVERT: A 1172 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.6435 (m90) REVERT: A 1190 ARG cc_start: 0.7182 (mpt180) cc_final: 0.6849 (mpt180) outliers start: 50 outliers final: 32 residues processed: 267 average time/residue: 0.0819 time to fit residues: 29.4835 Evaluate side-chains 292 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 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 586 MET Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE 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 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 987 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1047 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 Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1172 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 58 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115243 restraints weight = 13316.006| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.08 r_work: 0.3336 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2868 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= 0.149 Angle : 0.670 13.767 11506 Z= 0.334 Chirality : 0.041 0.187 1380 Planarity : 0.005 0.067 1415 Dihedral : 4.467 33.428 1135 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.86 % Allowed : 27.07 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.26), residues: 1039 helix: 1.64 (0.19), residues: 759 sheet: -0.44 (0.70), residues: 48 loop : -0.56 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 733 TYR 0.020 0.001 TYR A 267 PHE 0.042 0.002 PHE A 740 TRP 0.021 0.001 TRP A 763 HIS 0.008 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8482) covalent geometry : angle 0.66968 / 0.33 (11506) hydrogen bonds : bond 0.04772 / 3.23 ( 616) hydrogen bonds : angle 4.47611 / 3.20 ( 1833) ********************** 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 292 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.279 Fit side-chains REVERT: A 78 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7404 (mt) REVERT: A 116 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 195 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7285 (t80) REVERT: A 199 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7569 (mpp) REVERT: A 250 LYS cc_start: 0.8336 (mmmm) cc_final: 0.8029 (mtmm) REVERT: A 258 THR cc_start: 0.7284 (OUTLIER) cc_final: 0.6999 (p) REVERT: A 295 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7760 (t0) REVERT: A 337 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 359 LEU cc_start: 0.8710 (mt) cc_final: 0.8381 (mp) REVERT: A 380 VAL cc_start: 0.8302 (m) cc_final: 0.8028 (t) REVERT: A 383 MET cc_start: 0.6974 (mmm) cc_final: 0.6477 (mmm) REVERT: A 389 ILE cc_start: 0.8164 (mt) cc_final: 0.7900 (mm) REVERT: A 404 SER cc_start: 0.8356 (p) cc_final: 0.8129 (p) REVERT: A 581 GLU cc_start: 0.7671 (tp30) cc_final: 0.7333 (tp30) REVERT: A 606 GLU cc_start: 0.7716 (tp30) cc_final: 0.7361 (tp30) REVERT: A 678 MET cc_start: 0.6750 (tpp) cc_final: 0.6509 (mpp) REVERT: A 681 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 684 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 746 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: A 767 ASP cc_start: 0.7497 (m-30) cc_final: 0.7124 (p0) REVERT: A 800 LYS cc_start: 0.8312 (pttt) cc_final: 0.8069 (pptt) REVERT: A 810 MET cc_start: 0.5980 (tmm) cc_final: 0.5487 (tmm) REVERT: A 811 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5209 (pp) REVERT: A 854 ILE cc_start: 0.8615 (tp) cc_final: 0.8395 (tt) REVERT: A 943 ASN cc_start: 0.7689 (t0) cc_final: 0.7476 (t0) REVERT: A 1033 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7459 (mm-30) REVERT: A 1060 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7311 (mm-30) REVERT: A 1087 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: A 1113 THR cc_start: 0.8560 (t) cc_final: 0.8070 (p) REVERT: A 1116 LYS cc_start: 0.8145 (mtpm) cc_final: 0.7536 (mtpm) REVERT: A 1118 LYS cc_start: 0.6517 (tmtt) cc_final: 0.4993 (mtmt) REVERT: A 1122 GLU cc_start: 0.8123 (tp30) cc_final: 0.7745 (tp30) REVERT: A 1126 LEU cc_start: 0.8643 (mt) cc_final: 0.8437 (mp) REVERT: A 1190 ARG cc_start: 0.7172 (mpt180) cc_final: 0.6849 (mpt180) outliers start: 44 outliers final: 30 residues processed: 263 average time/residue: 0.0846 time to fit residues: 29.8934 Evaluate side-chains 286 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 251 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 586 MET Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 684 ILE 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 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 998 LEU Chi-restraints excluded: chain A residue 1000 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 97 optimal weight: 0.0770 chunk 21 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115329 restraints weight = 13348.125| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.08 r_work: 0.3351 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8482 Z= 0.151 Angle : 0.664 13.735 11506 Z= 0.330 Chirality : 0.041 0.178 1380 Planarity : 0.004 0.057 1415 Dihedral : 4.432 33.029 1135 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.53 % Allowed : 27.40 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 1039 helix: 1.66 (0.19), residues: 759 sheet: -0.46 (0.70), residues: 48 loop : -0.53 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1123 TYR 0.019 0.001 TYR A 267 PHE 0.040 0.002 PHE A 740 TRP 0.022 0.002 TRP A 763 HIS 0.009 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8482) covalent geometry : angle 0.66380 / 0.33 (11506) hydrogen bonds : bond 0.04758 / 3.21 ( 616) hydrogen bonds : angle 4.46027 / 3.19 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.20 seconds wall clock time: 32 minutes 19.90 seconds (1939.90 seconds total)