Starting phenix.real_space_refine on Sun May 11 05:48:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b91_44365/05_2025/9b91_44365.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b91_44365/05_2025/9b91_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b91_44365/05_2025/9b91_44365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b91_44365/05_2025/9b91_44365.map" model { file = "/net/cci-nas-00/data/ceres_data/9b91_44365/05_2025/9b91_44365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b91_44365/05_2025/9b91_44365.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 285 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.52, per 1000 atoms: 0.73 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: 2.28 Conformation dependent library (CDL) restraints added in 933.3 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: 0.78 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: 2.65 Time building geometry restraints manager: 2.61 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 2.510 nonbonded pdb=" OE1 GLN A 831 " pdb="CA CA A2001 " model vdw 2.170 2.510 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: 4.460 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (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 TRP 0.007 0.001 TRP A 213 HIS 0.003 0.001 HIS A 173 PHE 0.007 0.001 PHE A 223 TYR 0.007 0.001 TYR A1015 ARG 0.003 0.000 ARG A1062 Details of bonding type rmsd hydrogen bonds : bond 0.18732 ( 476) hydrogen bonds : angle 7.19904 ( 1383) SS BOND : bond 0.55820 ( 1) SS BOND : angle 23.59010 ( 2) covalent geometry : bond 0.00509 ( 7682) covalent geometry : angle 0.49942 (10459) *********************** 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 : 0.800 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: 0.1834 time to fit residues: 27.6631 Evaluate side-chains 66 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 83 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A1032 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.077004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.060616 restraints weight = 29018.777| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.05 r_work: 0.2982 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7683 Z= 0.140 Angle : 0.582 10.997 10461 Z= 0.296 Chirality : 0.038 0.160 1206 Planarity : 0.004 0.041 1315 Dihedral : 6.966 69.036 1108 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.07 % Allowed : 8.83 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 975 helix: 2.61 (0.21), residues: 621 sheet: -1.21 (0.64), residues: 64 loop : -0.34 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 772 HIS 0.002 0.001 HIS A 159 PHE 0.022 0.002 PHE A 249 TYR 0.010 0.001 TYR A 227 ARG 0.010 0.001 ARG A 601 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 476) hydrogen bonds : angle 4.59179 ( 1383) SS BOND : bond 0.00204 ( 1) SS BOND : angle 1.27741 ( 2) covalent geometry : bond 0.00309 ( 7682) covalent geometry : angle 0.58173 (10459) *********************** 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 99 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 784 MET cc_start: 0.9283 (ttm) cc_final: 0.9008 (tmm) REVERT: A 1034 LEU cc_start: 0.9185 (mp) cc_final: 0.8772 (tt) REVERT: A 1037 ASN cc_start: 0.9415 (m-40) cc_final: 0.9097 (m110) REVERT: A 1051 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8418 (tm-30) outliers start: 15 outliers final: 7 residues processed: 92 average time/residue: 0.1652 time to fit residues: 21.8610 Evaluate side-chains 73 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 505 HIS A 973 GLN A1032 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.076589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060245 restraints weight = 29277.668| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 4.02 r_work: 0.2991 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7683 Z= 0.126 Angle : 0.533 9.212 10461 Z= 0.272 Chirality : 0.036 0.159 1206 Planarity : 0.004 0.041 1315 Dihedral : 6.634 77.808 1108 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.21 % Allowed : 11.59 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.28), residues: 975 helix: 2.50 (0.21), residues: 623 sheet: -1.21 (0.64), residues: 64 loop : -0.45 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 61 HIS 0.003 0.001 HIS A 66 PHE 0.021 0.001 PHE A 697 TYR 0.009 0.001 TYR A 227 ARG 0.007 0.001 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 476) hydrogen bonds : angle 4.35341 ( 1383) SS BOND : bond 0.01189 ( 1) SS BOND : angle 1.49809 ( 2) covalent geometry : bond 0.00277 ( 7682) covalent geometry : angle 0.53269 (10459) *********************** 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 87 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8984 (ptp) cc_final: 0.8599 (ptp) REVERT: A 629 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 1034 LEU cc_start: 0.9180 (mp) cc_final: 0.8747 (tt) REVERT: A 1037 ASN cc_start: 0.9369 (m-40) cc_final: 0.9034 (m110) REVERT: A 1051 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8253 (tm-30) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.1447 time to fit residues: 17.6471 Evaluate side-chains 74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 657 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 69 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.076642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060468 restraints weight = 29205.202| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.03 r_work: 0.2965 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7683 Z= 0.123 Angle : 0.505 7.876 10461 Z= 0.256 Chirality : 0.036 0.147 1206 Planarity : 0.004 0.040 1315 Dihedral : 6.257 86.747 1108 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.33 % Rotamer: Outliers : 2.62 % Allowed : 12.83 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.28), residues: 975 helix: 2.58 (0.21), residues: 625 sheet: -1.29 (0.63), residues: 64 loop : -0.58 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.004 0.001 HIS A 505 PHE 0.023 0.001 PHE A 697 TYR 0.008 0.001 TYR A 227 ARG 0.006 0.000 ARG A1138 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 476) hydrogen bonds : angle 4.13537 ( 1383) SS BOND : bond 0.00238 ( 1) SS BOND : angle 1.36702 ( 2) covalent geometry : bond 0.00276 ( 7682) covalent geometry : angle 0.50435 (10459) *********************** 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 86 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.9455 (t0) cc_final: 0.9252 (t0) REVERT: A 186 MET cc_start: 0.9111 (ptp) cc_final: 0.8688 (ptp) REVERT: A 669 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8680 (mm110) REVERT: A 1034 LEU cc_start: 0.9191 (mp) cc_final: 0.8744 (tt) REVERT: A 1037 ASN cc_start: 0.9359 (m-40) cc_final: 0.9058 (m110) REVERT: A 1051 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8221 (tm-30) outliers start: 19 outliers final: 12 residues processed: 79 average time/residue: 0.1556 time to fit residues: 18.1576 Evaluate side-chains 75 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 636 VAL Chi-restraints excluded: chain A residue 657 LEU 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 Chi-restraints excluded: chain A residue 1032 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 240 HIS A 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.074861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.058566 restraints weight = 29091.186| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.01 r_work: 0.2929 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7683 Z= 0.157 Angle : 0.534 6.733 10461 Z= 0.271 Chirality : 0.036 0.148 1206 Planarity : 0.004 0.041 1315 Dihedral : 5.853 88.241 1105 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 2.76 % Allowed : 14.21 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 975 helix: 2.43 (0.21), residues: 639 sheet: -1.51 (0.60), residues: 70 loop : -0.72 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.007 0.001 HIS A 505 PHE 0.028 0.001 PHE A 373 TYR 0.009 0.001 TYR A 227 ARG 0.004 0.000 ARG A1138 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 476) hydrogen bonds : angle 4.14612 ( 1383) SS BOND : bond 0.00402 ( 1) SS BOND : angle 1.49188 ( 2) covalent geometry : bond 0.00358 ( 7682) covalent geometry : angle 0.53340 (10459) *********************** 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 80 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9172 (ptp) cc_final: 0.8819 (ptp) REVERT: A 669 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8694 (mm110) REVERT: A 1034 LEU cc_start: 0.9227 (mp) cc_final: 0.8738 (tt) REVERT: A 1037 ASN cc_start: 0.9358 (m-40) cc_final: 0.9055 (m110) REVERT: A 1051 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8258 (tm-30) outliers start: 20 outliers final: 14 residues processed: 75 average time/residue: 0.1616 time to fit residues: 18.0699 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 : 0.858 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1032 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 0.1980 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 27 optimal weight: 0.0970 chunk 34 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.072817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056547 restraints weight = 29348.379| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.91 r_work: 0.2881 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7683 Z= 0.213 Angle : 0.578 8.918 10461 Z= 0.293 Chirality : 0.038 0.151 1206 Planarity : 0.004 0.041 1315 Dihedral : 5.673 84.754 1105 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.03 % Allowed : 14.62 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.28), residues: 975 helix: 2.41 (0.21), residues: 637 sheet: -1.49 (0.59), residues: 69 loop : -0.72 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.003 0.001 HIS A 66 PHE 0.019 0.001 PHE A 697 TYR 0.010 0.001 TYR A 227 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 476) hydrogen bonds : angle 4.27282 ( 1383) SS BOND : bond 0.00466 ( 1) SS BOND : angle 1.72768 ( 2) covalent geometry : bond 0.00477 ( 7682) covalent geometry : angle 0.57792 (10459) *********************** 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 79 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9200 (ptp) cc_final: 0.8803 (ptp) REVERT: A 430 MET cc_start: 0.9629 (mmm) cc_final: 0.9322 (tpp) REVERT: A 784 MET cc_start: 0.9209 (ttm) cc_final: 0.8921 (tmm) REVERT: A 1037 ASN cc_start: 0.9433 (m-40) cc_final: 0.9131 (m110) REVERT: A 1051 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 1138 ARG cc_start: 0.9366 (ttp80) cc_final: 0.9127 (ttp80) outliers start: 22 outliers final: 16 residues processed: 74 average time/residue: 0.1460 time to fit residues: 16.3135 Evaluate side-chains 72 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 262 THR 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 904 VAL 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 0 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.074260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058052 restraints weight = 29035.595| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.99 r_work: 0.2940 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3518 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= 0.121 Angle : 0.516 9.278 10461 Z= 0.263 Chirality : 0.036 0.156 1206 Planarity : 0.004 0.038 1315 Dihedral : 5.488 80.795 1105 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.90 % Allowed : 15.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.28), residues: 975 helix: 2.61 (0.21), residues: 629 sheet: -1.87 (0.60), residues: 65 loop : -0.60 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 772 HIS 0.003 0.001 HIS A 66 PHE 0.018 0.001 PHE A 697 TYR 0.007 0.001 TYR A 227 ARG 0.009 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 476) hydrogen bonds : angle 4.09461 ( 1383) SS BOND : bond 0.00263 ( 1) SS BOND : angle 1.18114 ( 2) covalent geometry : bond 0.00276 ( 7682) covalent geometry : angle 0.51597 (10459) *********************** 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 85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8949 (tm-30) REVERT: A 186 MET cc_start: 0.9176 (ptp) cc_final: 0.8795 (ptp) REVERT: A 669 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8729 (mm110) REVERT: A 784 MET cc_start: 0.9169 (ttm) cc_final: 0.8895 (tmm) REVERT: A 988 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8203 (mtm) REVERT: A 1034 LEU cc_start: 0.9224 (mp) cc_final: 0.8721 (tt) REVERT: A 1037 ASN cc_start: 0.9377 (m-40) cc_final: 0.9090 (m110) REVERT: A 1051 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 1138 ARG cc_start: 0.9353 (ttp80) cc_final: 0.8806 (ttp80) outliers start: 21 outliers final: 14 residues processed: 77 average time/residue: 0.1487 time to fit residues: 17.3888 Evaluate side-chains 74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 262 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 657 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 84 optimal weight: 0.0040 chunk 8 optimal weight: 4.9990 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A1032 ASN A1061 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.073807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057544 restraints weight = 29768.488| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.98 r_work: 0.2895 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7683 Z= 0.194 Angle : 0.554 8.706 10461 Z= 0.282 Chirality : 0.037 0.162 1206 Planarity : 0.004 0.040 1315 Dihedral : 5.434 78.955 1105 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.31 % Allowed : 16.00 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.28), residues: 975 helix: 2.55 (0.21), residues: 628 sheet: -1.80 (0.61), residues: 64 loop : -0.65 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 680 HIS 0.003 0.001 HIS A 66 PHE 0.018 0.001 PHE A 697 TYR 0.008 0.001 TYR A 227 ARG 0.008 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 476) hydrogen bonds : angle 4.22262 ( 1383) SS BOND : bond 0.00455 ( 1) SS BOND : angle 1.67978 ( 2) covalent geometry : bond 0.00436 ( 7682) covalent geometry : angle 0.55344 (10459) *********************** 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 82 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8987 (tm-30) REVERT: A 186 MET cc_start: 0.9193 (ptp) cc_final: 0.8767 (ptp) REVERT: A 784 MET cc_start: 0.9181 (ttm) cc_final: 0.8905 (tmm) REVERT: A 1037 ASN cc_start: 0.9419 (m-40) cc_final: 0.9131 (m110) REVERT: A 1051 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 1138 ARG cc_start: 0.9377 (ttp80) cc_final: 0.9141 (ttp80) outliers start: 24 outliers final: 19 residues processed: 75 average time/residue: 0.1607 time to fit residues: 18.2444 Evaluate side-chains 77 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 510 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 657 LEU 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 1032 ASN 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 8 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 60 optimal weight: 0.0030 chunk 83 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3502 r_free = 0.3502 target = 0.074075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057901 restraints weight = 29772.449| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.02 r_work: 0.2928 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3790 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= 0.112 Angle : 0.532 9.384 10461 Z= 0.269 Chirality : 0.037 0.179 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.384 76.935 1105 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.90 % Allowed : 16.14 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.28), residues: 975 helix: 2.61 (0.21), residues: 628 sheet: -1.72 (0.63), residues: 64 loop : -0.68 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.010 0.001 HIS A 240 PHE 0.017 0.001 PHE A 697 TYR 0.007 0.001 TYR A1063 ARG 0.005 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 476) hydrogen bonds : angle 4.10420 ( 1383) SS BOND : bond 0.00275 ( 1) SS BOND : angle 1.12835 ( 2) covalent geometry : bond 0.00250 ( 7682) covalent geometry : angle 0.53179 (10459) *********************** 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 82 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8961 (tm-30) REVERT: A 186 MET cc_start: 0.9137 (ptp) cc_final: 0.8712 (ptp) REVERT: A 430 MET cc_start: 0.9628 (mmm) cc_final: 0.9311 (mpp) REVERT: A 580 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8519 (mt-10) REVERT: A 629 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 784 MET cc_start: 0.9137 (ttm) cc_final: 0.8861 (tmm) REVERT: A 1034 LEU cc_start: 0.9220 (mp) cc_final: 0.8702 (tt) REVERT: A 1037 ASN cc_start: 0.9361 (m-40) cc_final: 0.9070 (m110) REVERT: A 1051 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 1138 ARG cc_start: 0.9371 (ttp80) cc_final: 0.9152 (ttp80) outliers start: 21 outliers final: 18 residues processed: 75 average time/residue: 0.1573 time to fit residues: 17.8051 Evaluate side-chains 79 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 789 SER 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 1032 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.0040 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3479 r_free = 0.3479 target = 0.073223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057109 restraints weight = 29778.110| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.97 r_work: 0.2927 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7683 Z= 0.152 Angle : 0.543 9.574 10461 Z= 0.275 Chirality : 0.037 0.194 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.341 75.989 1105 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.62 % Allowed : 16.28 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.28), residues: 975 helix: 2.62 (0.21), residues: 628 sheet: -1.70 (0.63), residues: 64 loop : -0.75 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.008 0.001 HIS A 240 PHE 0.016 0.001 PHE A 697 TYR 0.007 0.001 TYR A 227 ARG 0.007 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 476) hydrogen bonds : angle 4.11674 ( 1383) SS BOND : bond 0.00315 ( 1) SS BOND : angle 1.31734 ( 2) covalent geometry : bond 0.00348 ( 7682) covalent geometry : angle 0.54314 (10459) ********************** 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 80 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7991 (tm-30) REVERT: A 135 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8964 (tm-30) REVERT: A 186 MET cc_start: 0.9150 (ptp) cc_final: 0.8716 (ptp) REVERT: A 629 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 784 MET cc_start: 0.9146 (ttm) cc_final: 0.8888 (tmm) REVERT: A 1034 LEU cc_start: 0.9254 (mp) cc_final: 0.8734 (tt) REVERT: A 1037 ASN cc_start: 0.9382 (m-40) cc_final: 0.9099 (m110) REVERT: A 1051 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 1138 ARG cc_start: 0.9384 (ttp80) cc_final: 0.9160 (ttp80) outliers start: 19 outliers final: 18 residues processed: 75 average time/residue: 0.1573 time to fit residues: 17.8062 Evaluate side-chains 78 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 510 LEU Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 789 SER 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 1032 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.073803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.057696 restraints weight = 29464.107| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.00 r_work: 0.2931 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3900 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= 0.118 Angle : 0.532 9.537 10461 Z= 0.269 Chirality : 0.037 0.203 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.327 74.787 1105 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.62 % Allowed : 16.28 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.28), residues: 975 helix: 2.60 (0.21), residues: 628 sheet: -1.61 (0.64), residues: 64 loop : -0.73 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 772 HIS 0.003 0.001 HIS A 66 PHE 0.016 0.001 PHE A 697 TYR 0.006 0.001 TYR A 227 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 476) hydrogen bonds : angle 4.10551 ( 1383) SS BOND : bond 0.00259 ( 1) SS BOND : angle 1.06023 ( 2) covalent geometry : bond 0.00268 ( 7682) covalent geometry : angle 0.53205 (10459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.61 seconds wall clock time: 62 minutes 44.39 seconds (3764.39 seconds total)