Starting phenix.real_space_refine on Thu Jul 2 07:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b91_44365/07_2026/9b91_44365.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b91_44365/07_2026/9b91_44365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b91_44365/07_2026/9b91_44365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b91_44365/07_2026/9b91_44365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b91_44365/07_2026/9b91_44365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b91_44365/07_2026/9b91_44365.map" } resolution = 3.3 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= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 3 5.49 5 S 38 5.16 5 C 4854 2.51 5 N 1327 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7511 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7478 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 19, 'TRP:plan': 1, 'GLN:plan1': 5, 'ARG:plan': 15, 'ASP:plan': 19, 'HIS:plan': 3, 'PHE:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 285 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7511 At special positions: 0 Unit cell: (87.768, 120.06, 153.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 38 16.00 P 3 15.00 O 1287 8.00 N 1327 7.00 C 4854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.59 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: 0.67 Conformation dependent library (CDL) restraints added in 387.2 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 67.7% alpha, 4.5% 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 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.650A pdb=" N ILE A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.884A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.724A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.951A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.294A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.508A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 421 through 435 removed outlier: 4.076A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.589A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 removed outlier: 3.645A pdb=" N ARG A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 645 removed outlier: 3.541A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.557A pdb=" N THR A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 778 removed outlier: 3.526A pdb=" N ALA A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.847A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 905 Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 916 through 926 Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 974 removed outlier: 3.624A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.883A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1071 removed outlier: 4.877A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.267A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1143 Processing helix chain 'A' and resid 1143 through 1176 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 156 removed outlier: 6.165A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR A 211 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.550A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991 removed outlier: 4.062A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1383 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: 1.32 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2433 1.34 - 1.46: 1693 1.46 - 1.57: 3494 1.57 - 1.69: 5 1.69 - 1.81: 57 Bond restraints: 7682 Sorted by residual: bond pdb=" CB THR A 823 " pdb=" CG2 THR A 823 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CB TRP A1124 " pdb=" CG TRP A1124 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.34e+00 bond pdb=" CB GLN A 669 " pdb=" CG GLN A 669 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB TRP A 681 " pdb=" CG TRP A 681 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.61e-01 bond pdb=" CB CYS A1011 " pdb=" SG CYS A1011 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.17e-01 ... (remaining 7677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 10227 1.27 - 2.55: 171 2.55 - 3.82: 45 3.82 - 5.10: 12 5.10 - 6.37: 4 Bond angle restraints: 10459 Sorted by residual: angle pdb=" C3' ATP A2003 " pdb=" C4' ATP A2003 " pdb=" C5' ATP A2003 " ideal model delta sigma weight residual 115.19 110.95 4.24 1.76e+00 3.23e-01 5.81e+00 angle pdb=" C2' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" O3' ATP A2003 " ideal model delta sigma weight residual 111.83 105.58 6.25 2.67e+00 1.40e-01 5.48e+00 angle pdb=" N GLY A 220 " pdb=" CA GLY A 220 " pdb=" C GLY A 220 " ideal model delta sigma weight residual 110.77 115.28 -4.51 1.93e+00 2.68e-01 5.46e+00 angle pdb=" C1' ATP A2003 " pdb=" C2' ATP A2003 " pdb=" O2' ATP A2003 " ideal model delta sigma weight residual 110.58 104.21 6.37 2.79e+00 1.28e-01 5.20e+00 angle pdb=" C3' ATP A2003 " pdb=" C2' ATP A2003 " pdb=" O2' ATP A2003 " ideal model delta sigma weight residual 111.83 106.09 5.74 2.67e+00 1.40e-01 4.62e+00 ... (remaining 10454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 4256 16.86 - 33.72: 205 33.72 - 50.59: 41 50.59 - 67.45: 19 67.45 - 84.31: 5 Dihedral angle restraints: 4526 sinusoidal: 1679 harmonic: 2847 Sorted by residual: dihedral pdb=" CB CYS A 993 " pdb=" SG CYS A 993 " pdb=" SG CYS A1011 " pdb=" CB CYS A1011 " ideal model delta sinusoidal sigma weight residual -86.00 -146.15 60.15 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG A 139 " pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " pdb=" CD ARG A 139 " ideal model delta sinusoidal sigma weight residual -60.00 -118.74 58.74 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1097 0.059 - 0.117: 101 0.117 - 0.176: 5 0.176 - 0.235: 0 0.235 - 0.294: 3 Chirality restraints: 1206 Sorted by residual: chirality pdb=" C2' ATP A2003 " pdb=" C1' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" O2' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' ATP A2003 " pdb=" C2' ATP A2003 " pdb=" C4' ATP A2003 " pdb=" O3' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C4' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" C5' ATP A2003 " pdb=" O4' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1203 not shown) Planarity restraints: 1315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 699 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 700 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 700 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 700 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1076 " 0.016 5.00e-02 4.00e+02 2.34e-02 8.79e-01 pdb=" N PRO A1077 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 456 " -0.013 5.00e-02 4.00e+02 1.94e-02 6.05e-01 pdb=" N PRO A 457 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " -0.011 5.00e-02 4.00e+02 ... (remaining 1312 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 143 2.67 - 3.23: 8232 3.23 - 3.79: 11978 3.79 - 4.34: 14841 4.34 - 4.90: 24713 Nonbonded interactions: 59907 Sorted by model distance: nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.119 3.250 nonbonded pdb=" OE1 GLN A 831 " pdb="CA CA A2001 " model vdw 2.170 3.250 nonbonded pdb=" N GLU A 374 " pdb=" OE1 GLU A 374 " model vdw 2.204 3.120 nonbonded pdb=" O PHE A 454 " pdb=" NH1 ARG A 459 " model vdw 2.236 3.120 nonbonded pdb=" N GLU A 389 " pdb=" OE1 GLU A 389 " model vdw 2.238 3.120 ... (remaining 59902 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: 3.840 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.460 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.008 0.558 7683 Z= 0.400 Angle : 0.596 26.759 10461 Z= 0.311 Chirality : 0.036 0.294 1206 Planarity : 0.003 0.041 1315 Dihedral : 11.380 84.310 2683 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.28 % Allowed : 5.79 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.45 (0.27), residues: 975 helix: 2.00 (0.21), residues: 605 sheet: -2.01 (0.59), residues: 59 loop : -0.46 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1062 TYR 0.007 0.001 TYR A1015 PHE 0.007 0.001 PHE A 223 TRP 0.007 0.001 TRP A 213 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 ( 7682) covalent geometry : angle 0.49942 / 0.27 (10459) SS BOND : bond 0.55820 / 29.38 ( 1) SS BOND : angle 23.59010 / 13.37 ( 2) hydrogen bonds : bond 0.18732 / 12.38 ( 476) hydrogen bonds : angle 7.19904 / 5.20 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1037 ASN cc_start: 0.8974 (m-40) cc_final: 0.8671 (m110) REVERT: A 1038 LEU cc_start: 0.9535 (tp) cc_final: 0.9307 (tt) outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.0830 time to fit residues: 12.6535 Evaluate side-chains 64 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 373 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 973 GLN A1032 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.076061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059526 restraints weight = 29633.161| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.08 r_work: 0.2958 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7683 Z= 0.166 Angle : 0.587 10.920 10461 Z= 0.302 Chirality : 0.038 0.168 1206 Planarity : 0.004 0.042 1315 Dihedral : 6.971 69.278 1108 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.21 % Allowed : 8.97 % Favored : 88.83 % 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: 2.31 (0.28), residues: 975 helix: 2.64 (0.21), residues: 620 sheet: -0.74 (0.67), residues: 57 loop : -0.41 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 601 TYR 0.009 0.001 TYR A 227 PHE 0.022 0.001 PHE A 697 TRP 0.011 0.001 TRP A 772 HIS 0.003 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 7682) covalent geometry : angle 0.58723 / 0.30 (10459) SS BOND : bond 0.00197 / 0.10 ( 1) SS BOND : angle 1.00491 / 0.54 ( 2) hydrogen bonds : bond 0.04365 / 3.02 ( 476) hydrogen bonds : angle 4.62739 / 3.30 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1034 LEU cc_start: 0.9178 (mp) cc_final: 0.8755 (tt) REVERT: A 1037 ASN cc_start: 0.9409 (m-40) cc_final: 0.9098 (m110) REVERT: A 1051 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 16 outliers final: 7 residues processed: 89 average time/residue: 0.0688 time to fit residues: 8.9062 Evaluate side-chains 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 904 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 HIS A1032 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.074340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057988 restraints weight = 29318.641| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.98 r_work: 0.2922 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7683 Z= 0.194 Angle : 0.566 8.654 10461 Z= 0.291 Chirality : 0.038 0.151 1206 Planarity : 0.005 0.060 1315 Dihedral : 6.640 79.342 1108 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.48 % Allowed : 11.45 % Favored : 86.07 % 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: 2.10 (0.28), residues: 975 helix: 2.51 (0.21), residues: 622 sheet: -1.33 (0.62), residues: 64 loop : -0.46 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 327 TYR 0.011 0.001 TYR A 227 PHE 0.022 0.001 PHE A 697 TRP 0.017 0.001 TRP A 61 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 7682) covalent geometry : angle 0.56536 / 0.29 (10459) SS BOND : bond 0.02480 / 1.31 ( 1) SS BOND : angle 1.62481 / 0.91 ( 2) hydrogen bonds : bond 0.04020 / 2.78 ( 476) hydrogen bonds : angle 4.39545 / 3.14 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9184 (ptp) cc_final: 0.8901 (ptp) REVERT: A 599 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8740 (ttm) REVERT: A 622 MET cc_start: 0.9255 (ptm) cc_final: 0.9019 (ptm) REVERT: A 1034 LEU cc_start: 0.9194 (mp) cc_final: 0.8710 (tt) REVERT: A 1037 ASN cc_start: 0.9409 (m-40) cc_final: 0.9099 (m110) REVERT: A 1051 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8302 (tm-30) outliers start: 18 outliers final: 11 residues processed: 80 average time/residue: 0.0695 time to fit residues: 8.3134 Evaluate side-chains 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1032 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 71 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 HIS A1032 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.075262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.059104 restraints weight = 29569.893| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.00 r_work: 0.2933 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7683 Z= 0.132 Angle : 0.527 7.965 10461 Z= 0.268 Chirality : 0.036 0.149 1206 Planarity : 0.004 0.042 1315 Dihedral : 6.323 86.240 1107 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.46 % Favored : 97.44 % Rotamer: Outliers : 2.48 % Allowed : 13.24 % Favored : 84.28 % 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: 2.16 (0.28), residues: 975 helix: 2.58 (0.21), residues: 621 sheet: -1.37 (0.62), residues: 64 loop : -0.47 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.010 0.001 TYR A 227 PHE 0.024 0.001 PHE A 697 TRP 0.009 0.001 TRP A 680 HIS 0.006 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7682) covalent geometry : angle 0.52624 / 0.27 (10459) SS BOND : bond 0.00180 / 0.09 ( 1) SS BOND : angle 1.50503 / 0.84 ( 2) hydrogen bonds : bond 0.03595 / 2.46 ( 476) hydrogen bonds : angle 4.23945 / 3.03 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9184 (ptp) cc_final: 0.8857 (ptp) REVERT: A 599 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8786 (ttm) REVERT: A 1037 ASN cc_start: 0.9399 (m-40) cc_final: 0.9081 (m110) REVERT: A 1051 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8260 (tm-30) outliers start: 18 outliers final: 8 residues processed: 71 average time/residue: 0.0689 time to fit residues: 7.3805 Evaluate side-chains 65 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 988 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.073676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057381 restraints weight = 29431.036| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.97 r_work: 0.2903 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7683 Z= 0.170 Angle : 0.537 7.009 10461 Z= 0.272 Chirality : 0.037 0.161 1206 Planarity : 0.004 0.040 1315 Dihedral : 5.921 87.274 1105 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.90 % Allowed : 13.66 % Favored : 83.45 % 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: 1.95 (0.28), residues: 975 helix: 2.43 (0.21), residues: 632 sheet: -1.60 (0.59), residues: 70 loop : -0.65 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1138 TYR 0.009 0.001 TYR A 227 PHE 0.027 0.001 PHE A 373 TRP 0.010 0.001 TRP A 680 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 7682) covalent geometry : angle 0.53671 / 0.27 (10459) SS BOND : bond 0.00399 / 0.21 ( 1) SS BOND : angle 1.55872 / 0.89 ( 2) hydrogen bonds : bond 0.03598 / 2.45 ( 476) hydrogen bonds : angle 4.21499 / 3.03 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9220 (ptp) cc_final: 0.8884 (ptp) REVERT: A 1034 LEU cc_start: 0.9254 (mp) cc_final: 0.8757 (tt) REVERT: A 1037 ASN cc_start: 0.9383 (m-40) cc_final: 0.9080 (m110) REVERT: A 1051 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8233 (tm-30) outliers start: 21 outliers final: 14 residues processed: 72 average time/residue: 0.0733 time to fit residues: 7.7171 Evaluate side-chains 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 988 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 HIS A 240 HIS A1032 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.075122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058914 restraints weight = 29426.349| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.04 r_work: 0.2943 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7683 Z= 0.111 Angle : 0.503 7.278 10461 Z= 0.256 Chirality : 0.035 0.153 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.631 83.084 1105 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 14.62 % Favored : 82.90 % 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: 2.13 (0.28), residues: 975 helix: 2.60 (0.21), residues: 629 sheet: -1.54 (0.59), residues: 70 loop : -0.63 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1138 TYR 0.007 0.001 TYR A 227 PHE 0.018 0.001 PHE A 373 TRP 0.009 0.001 TRP A 772 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 7682) covalent geometry : angle 0.50327 / 0.26 (10459) SS BOND : bond 0.00222 / 0.12 ( 1) SS BOND : angle 1.08190 / 0.62 ( 2) hydrogen bonds : bond 0.03282 / 2.23 ( 476) hydrogen bonds : angle 4.07554 / 2.92 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9210 (ptp) cc_final: 0.8866 (ptp) REVERT: A 327 ARG cc_start: 0.9205 (tpt170) cc_final: 0.8976 (tmm160) REVERT: A 1034 LEU cc_start: 0.9234 (mp) cc_final: 0.8745 (tt) REVERT: A 1037 ASN cc_start: 0.9343 (m-40) cc_final: 0.9048 (m110) REVERT: A 1051 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8141 (tm-30) outliers start: 18 outliers final: 14 residues processed: 76 average time/residue: 0.0683 time to fit residues: 7.8480 Evaluate side-chains 73 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1032 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 0.0030 chunk 80 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS A1061 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058997 restraints weight = 29326.376| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.04 r_work: 0.2953 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7683 Z= 0.109 Angle : 0.506 6.475 10461 Z= 0.257 Chirality : 0.035 0.160 1206 Planarity : 0.004 0.038 1315 Dihedral : 5.493 81.551 1105 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.17 % Allowed : 15.31 % Favored : 81.52 % 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: 2.15 (0.28), residues: 975 helix: 2.59 (0.21), residues: 629 sheet: -1.46 (0.59), residues: 70 loop : -0.58 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1138 TYR 0.006 0.001 TYR A 227 PHE 0.018 0.001 PHE A 697 TRP 0.009 0.001 TRP A 680 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7682) covalent geometry : angle 0.50536 / 0.26 (10459) SS BOND : bond 0.00241 / 0.13 ( 1) SS BOND : angle 1.03339 / 0.59 ( 2) hydrogen bonds : bond 0.03203 / 2.17 ( 476) hydrogen bonds : angle 4.04608 / 2.91 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9206 (ptp) cc_final: 0.8833 (ptp) REVERT: A 327 ARG cc_start: 0.9226 (tpt170) cc_final: 0.8967 (tmm160) REVERT: A 1034 LEU cc_start: 0.9221 (mp) cc_final: 0.8724 (tt) REVERT: A 1037 ASN cc_start: 0.9360 (m-40) cc_final: 0.9077 (m110) REVERT: A 1051 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8116 (tm-30) outliers start: 23 outliers final: 17 residues processed: 79 average time/residue: 0.0676 time to fit residues: 8.1118 Evaluate side-chains 79 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1061 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 0.0170 chunk 3 optimal weight: 0.2980 chunk 81 optimal weight: 0.0870 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS A1032 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.075348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059123 restraints weight = 29647.981| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 4.07 r_work: 0.2961 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7683 Z= 0.109 Angle : 0.500 6.444 10461 Z= 0.255 Chirality : 0.036 0.167 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.407 80.452 1105 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 16.00 % Favored : 81.52 % 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: 2.15 (0.28), residues: 975 helix: 2.60 (0.21), residues: 630 sheet: -1.80 (0.61), residues: 65 loop : -0.53 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1138 TYR 0.006 0.001 TYR A1063 PHE 0.017 0.001 PHE A 697 TRP 0.009 0.001 TRP A1124 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7682) covalent geometry : angle 0.50001 / 0.25 (10459) SS BOND : bond 0.00232 / 0.12 ( 1) SS BOND : angle 0.99969 / 0.58 ( 2) hydrogen bonds : bond 0.03164 / 2.15 ( 476) hydrogen bonds : angle 4.02522 / 2.89 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7910 (tm-30) REVERT: A 186 MET cc_start: 0.9221 (ptp) cc_final: 0.8836 (ptp) REVERT: A 327 ARG cc_start: 0.9247 (tpt170) cc_final: 0.9001 (tmm160) REVERT: A 988 MET cc_start: 0.8655 (mtt) cc_final: 0.8212 (mtm) REVERT: A 1034 LEU cc_start: 0.9217 (mp) cc_final: 0.8695 (tt) REVERT: A 1037 ASN cc_start: 0.9322 (m-40) cc_final: 0.9032 (m110) outliers start: 18 outliers final: 14 residues processed: 74 average time/residue: 0.0725 time to fit residues: 7.8872 Evaluate side-chains 74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1061 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.074030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057682 restraints weight = 29709.909| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.02 r_work: 0.2928 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7683 Z= 0.169 Angle : 0.522 6.526 10461 Z= 0.267 Chirality : 0.037 0.171 1206 Planarity : 0.004 0.040 1315 Dihedral : 5.377 79.837 1105 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.62 % Allowed : 16.00 % Favored : 81.38 % 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: 2.15 (0.28), residues: 975 helix: 2.63 (0.21), residues: 629 sheet: -1.81 (0.61), residues: 65 loop : -0.58 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1138 TYR 0.007 0.001 TYR A 227 PHE 0.015 0.001 PHE A 697 TRP 0.009 0.001 TRP A1124 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 7682) covalent geometry : angle 0.52173 / 0.27 (10459) SS BOND : bond 0.00375 / 0.20 ( 1) SS BOND : angle 1.39648 / 0.81 ( 2) hydrogen bonds : bond 0.03347 / 2.29 ( 476) hydrogen bonds : angle 4.09724 / 2.94 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7918 (tm-30) REVERT: A 186 MET cc_start: 0.9217 (ptp) cc_final: 0.8835 (ptp) REVERT: A 327 ARG cc_start: 0.9219 (tpt170) cc_final: 0.8982 (tmm160) REVERT: A 1034 LEU cc_start: 0.9264 (mp) cc_final: 0.8736 (tt) REVERT: A 1037 ASN cc_start: 0.9364 (m-40) cc_final: 0.9086 (m110) REVERT: A 1051 GLN cc_start: 0.8263 (tt0) cc_final: 0.7525 (tm-30) REVERT: A 1138 ARG cc_start: 0.9347 (ttp80) cc_final: 0.9113 (ttp80) outliers start: 19 outliers final: 14 residues processed: 74 average time/residue: 0.0672 time to fit residues: 7.5286 Evaluate side-chains 72 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS A1061 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.074278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058077 restraints weight = 29429.287| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.02 r_work: 0.2942 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7683 Z= 0.122 Angle : 0.513 7.097 10461 Z= 0.262 Chirality : 0.036 0.189 1206 Planarity : 0.004 0.040 1315 Dihedral : 5.352 78.315 1105 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.34 % Allowed : 16.00 % Favored : 81.66 % 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: 2.17 (0.28), residues: 975 helix: 2.64 (0.21), residues: 629 sheet: -1.75 (0.61), residues: 65 loop : -0.59 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1138 TYR 0.006 0.001 TYR A 227 PHE 0.016 0.001 PHE A 697 TRP 0.009 0.001 TRP A1124 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7682) covalent geometry : angle 0.51330 / 0.26 (10459) SS BOND : bond 0.00256 / 0.13 ( 1) SS BOND : angle 1.05450 / 0.61 ( 2) hydrogen bonds : bond 0.03248 / 2.20 ( 476) hydrogen bonds : angle 4.05915 / 2.92 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7926 (tm-30) REVERT: A 186 MET cc_start: 0.9214 (ptp) cc_final: 0.8832 (ptp) REVERT: A 327 ARG cc_start: 0.9235 (tpt170) cc_final: 0.8983 (tmt170) REVERT: A 988 MET cc_start: 0.8795 (mtt) cc_final: 0.8324 (mtm) REVERT: A 1034 LEU cc_start: 0.9240 (mp) cc_final: 0.8712 (tt) REVERT: A 1037 ASN cc_start: 0.9339 (m-40) cc_final: 0.9047 (m110) REVERT: A 1051 GLN cc_start: 0.8222 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 1138 ARG cc_start: 0.9341 (ttp80) cc_final: 0.9101 (ttp80) outliers start: 17 outliers final: 14 residues processed: 70 average time/residue: 0.0649 time to fit residues: 6.8944 Evaluate side-chains 71 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1061 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.074231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058077 restraints weight = 29270.448| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.00 r_work: 0.2933 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 7683 Z= 0.254 Angle : 0.927 59.123 10461 Z= 0.557 Chirality : 0.037 0.198 1206 Planarity : 0.005 0.094 1315 Dihedral : 5.348 78.309 1105 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.07 % Allowed : 16.00 % Favored : 81.93 % Cbeta Deviations : 0.11 % 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: 2.16 (0.28), residues: 975 helix: 2.63 (0.21), residues: 629 sheet: -1.75 (0.61), residues: 65 loop : -0.59 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.007 0.001 TYR A 227 PHE 0.018 0.001 PHE A 697 TRP 0.009 0.001 TRP A1124 HIS 0.132 0.005 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.25 ( 7682) covalent geometry : angle 0.92747 / 0.56 (10459) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 1.02604 / 0.59 ( 2) hydrogen bonds : bond 0.03275 / 2.21 ( 476) hydrogen bonds : angle 4.06503 / 2.93 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1981.72 seconds wall clock time: 34 minutes 44.43 seconds (2084.43 seconds total)