Starting phenix.real_space_refine on Wed Sep 17 09:15:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b91_44365/09_2025/9b91_44365.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b91_44365/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b91_44365/09_2025/9b91_44365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b91_44365/09_2025/9b91_44365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b91_44365/09_2025/9b91_44365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b91_44365/09_2025/9b91_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-2.0-5805/lib/python3.9/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, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.07, per 1000 atoms: 0.28 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: 0.65 Conformation dependent library (CDL) restraints added in 338.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.31 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: 1.31 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 3.900 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00509 ( 7682) covalent geometry : angle 0.49942 (10459) SS BOND : bond 0.55820 ( 1) SS BOND : angle 23.59010 ( 2) hydrogen bonds : bond 0.18732 ( 476) hydrogen bonds : angle 7.19904 ( 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 : 0.290 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: 0.0861 time to fit residues: 13.0694 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 : 0.292 ------------------------------------------------------------------------------- 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... 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 = 0.3525 r_free = 0.3525 target = 0.076003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059370 restraints weight = 29707.576| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.08 r_work: 0.2960 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7683 Z= 0.164 Angle : 0.587 11.257 10461 Z= 0.300 Chirality : 0.038 0.164 1206 Planarity : 0.004 0.042 1315 Dihedral : 7.011 68.341 1108 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.07 % Allowed : 9.10 % 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 aren not related in a simple way. whole: 2.31 (0.28), residues: 975 helix: 2.63 (0.21), residues: 620 sheet: -0.76 (0.67), residues: 57 loop : -0.41 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 601 TYR 0.010 0.001 TYR A 227 PHE 0.023 0.001 PHE A 697 TRP 0.011 0.001 TRP A 772 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7682) covalent geometry : angle 0.58719 (10459) SS BOND : bond 0.00520 ( 1) SS BOND : angle 1.37386 ( 2) hydrogen bonds : bond 0.04482 ( 476) hydrogen bonds : angle 4.65008 ( 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: 15 poor density : 82 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 PHE cc_start: 0.9370 (t80) cc_final: 0.9060 (t80) REVERT: A 784 MET cc_start: 0.9296 (ttm) cc_final: 0.8875 (tmm) REVERT: A 1034 LEU cc_start: 0.9188 (mp) cc_final: 0.8773 (tt) REVERT: A 1037 ASN cc_start: 0.9414 (m-40) cc_final: 0.9107 (m110) REVERT: A 1051 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8465 (tm-30) outliers start: 15 outliers final: 8 residues processed: 90 average time/residue: 0.0813 time to fit residues: 10.4097 Evaluate side-chains 71 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 562 LEU 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: 3.9990 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A 973 GLN A1032 ASN 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 = 0.075058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058614 restraints weight = 29345.211| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.02 r_work: 0.2941 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7683 Z= 0.175 Angle : 0.554 9.022 10461 Z= 0.284 Chirality : 0.037 0.149 1206 Planarity : 0.004 0.045 1315 Dihedral : 6.685 77.584 1108 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.21 % Allowed : 11.31 % Favored : 86.48 % 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 aren not related in a simple way. whole: 2.11 (0.28), residues: 975 helix: 2.52 (0.21), residues: 622 sheet: -1.31 (0.62), residues: 64 loop : -0.46 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 327 TYR 0.010 0.001 TYR A 227 PHE 0.016 0.001 PHE A 697 TRP 0.013 0.001 TRP A 61 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 7682) covalent geometry : angle 0.55365 (10459) SS BOND : bond 0.00644 ( 1) SS BOND : angle 1.73512 ( 2) hydrogen bonds : bond 0.03999 ( 476) hydrogen bonds : angle 4.42145 ( 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 82 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9138 (ptp) cc_final: 0.8834 (ptp) REVERT: A 622 MET cc_start: 0.9198 (ptm) cc_final: 0.8996 (ptm) REVERT: A 1034 LEU cc_start: 0.9192 (mp) cc_final: 0.8725 (tt) REVERT: A 1037 ASN cc_start: 0.9413 (m-40) cc_final: 0.9099 (m110) REVERT: A 1051 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8328 (tm-30) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.0740 time to fit residues: 8.4415 Evaluate side-chains 72 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 74 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3517 r_free = 0.3517 target = 0.074919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058701 restraints weight = 29721.024| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.99 r_work: 0.2926 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7683 Z= 0.155 Angle : 0.539 7.905 10461 Z= 0.274 Chirality : 0.036 0.154 1206 Planarity : 0.004 0.042 1315 Dihedral : 6.374 84.297 1107 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.62 % Allowed : 12.97 % Favored : 84.41 % 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 aren not related in a simple way. whole: 2.13 (0.28), residues: 975 helix: 2.54 (0.21), residues: 621 sheet: -1.40 (0.62), residues: 64 loop : -0.43 (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 0.015 0.001 PHE A 697 TRP 0.009 0.001 TRP A 680 HIS 0.009 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7682) covalent geometry : angle 0.53833 (10459) SS BOND : bond 0.00368 ( 1) SS BOND : angle 1.61488 ( 2) hydrogen bonds : bond 0.03705 ( 476) hydrogen bonds : angle 4.31999 ( 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 80 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9157 (ptp) cc_final: 0.8840 (ptp) REVERT: A 599 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8820 (ttm) REVERT: A 1037 ASN cc_start: 0.9410 (m-40) cc_final: 0.9096 (m110) REVERT: A 1051 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8326 (tm-30) outliers start: 19 outliers final: 9 residues processed: 73 average time/residue: 0.0699 time to fit residues: 7.5703 Evaluate side-chains 65 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 2 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.074905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058635 restraints weight = 29293.879| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.05 r_work: 0.2925 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3131 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= 0.138 Angle : 0.520 7.059 10461 Z= 0.264 Chirality : 0.036 0.150 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.971 87.987 1105 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.62 % Allowed : 13.52 % Favored : 83.86 % 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 aren not related in a simple way. whole: 1.99 (0.28), residues: 975 helix: 2.44 (0.21), residues: 638 sheet: -1.58 (0.59), residues: 70 loop : -0.65 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.008 0.001 TYR A 227 PHE 0.028 0.001 PHE A 373 TRP 0.009 0.001 TRP A 680 HIS 0.005 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7682) covalent geometry : angle 0.51936 (10459) SS BOND : bond 0.00333 ( 1) SS BOND : angle 1.35645 ( 2) hydrogen bonds : bond 0.03470 ( 476) hydrogen bonds : angle 4.16723 ( 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 81 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9208 (ptp) cc_final: 0.8886 (ptp) REVERT: A 327 ARG cc_start: 0.9258 (tpt170) cc_final: 0.9012 (tmm160) REVERT: A 599 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8825 (ttm) REVERT: A 784 MET cc_start: 0.9177 (ttm) cc_final: 0.8888 (tmm) REVERT: A 1034 LEU cc_start: 0.9232 (mp) cc_final: 0.8774 (tt) REVERT: A 1037 ASN cc_start: 0.9364 (m-40) cc_final: 0.9079 (m110) REVERT: A 1051 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8240 (tm-30) outliers start: 19 outliers final: 12 residues processed: 76 average time/residue: 0.0699 time to fit residues: 7.8630 Evaluate side-chains 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A1032 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.074903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.058614 restraints weight = 29426.673| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.05 r_work: 0.2952 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7683 Z= 0.121 Angle : 0.498 6.503 10461 Z= 0.254 Chirality : 0.035 0.157 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.620 83.714 1105 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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 aren not related in a simple way. whole: 2.04 (0.28), residues: 975 helix: 2.50 (0.21), residues: 639 sheet: -1.50 (0.59), residues: 70 loop : -0.72 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1138 TYR 0.007 0.001 TYR A 227 PHE 0.017 0.001 PHE A 373 TRP 0.009 0.001 TRP A 772 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7682) covalent geometry : angle 0.49827 (10459) SS BOND : bond 0.00267 ( 1) SS BOND : angle 1.16847 ( 2) hydrogen bonds : bond 0.03300 ( 476) hydrogen bonds : angle 4.06705 ( 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 82 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8915 (tm-30) REVERT: A 186 MET cc_start: 0.9216 (ptp) cc_final: 0.8860 (ptp) REVERT: A 327 ARG cc_start: 0.9215 (tpt170) cc_final: 0.8998 (tmm160) REVERT: A 784 MET cc_start: 0.9149 (ttm) cc_final: 0.8876 (tmm) REVERT: A 1034 LEU cc_start: 0.9225 (mp) cc_final: 0.8736 (tt) REVERT: A 1037 ASN cc_start: 0.9332 (m-40) cc_final: 0.9043 (m110) REVERT: A 1051 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8206 (tm-30) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.0736 time to fit residues: 8.1969 Evaluate side-chains 71 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 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 988 MET 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: 0.8980 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.074530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058186 restraints weight = 29574.382| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.04 r_work: 0.2937 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7683 Z= 0.129 Angle : 0.502 6.558 10461 Z= 0.256 Chirality : 0.036 0.163 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.486 82.238 1105 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.17 % Allowed : 15.17 % 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 aren not related in a simple way. whole: 2.04 (0.28), residues: 975 helix: 2.49 (0.21), residues: 639 sheet: -1.48 (0.59), residues: 70 loop : -0.69 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1138 TYR 0.007 0.001 TYR A 227 PHE 0.015 0.001 PHE A 373 TRP 0.009 0.001 TRP A 680 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7682) covalent geometry : angle 0.50153 (10459) SS BOND : bond 0.00296 ( 1) SS BOND : angle 1.22367 ( 2) hydrogen bonds : bond 0.03301 ( 476) hydrogen bonds : angle 4.08206 ( 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 83 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8928 (tm-30) REVERT: A 186 MET cc_start: 0.9200 (ptp) cc_final: 0.8833 (ptp) REVERT: A 327 ARG cc_start: 0.9174 (tpt170) cc_final: 0.8971 (tmt170) REVERT: A 574 MET cc_start: 0.9385 (mmm) cc_final: 0.9062 (mmt) REVERT: A 784 MET cc_start: 0.9154 (ttm) cc_final: 0.8888 (tmm) REVERT: A 1034 LEU cc_start: 0.9224 (mp) cc_final: 0.8733 (tt) REVERT: A 1037 ASN cc_start: 0.9357 (m-40) cc_final: 0.9084 (m110) REVERT: A 1051 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8209 (tm-30) outliers start: 23 outliers final: 17 residues processed: 75 average time/residue: 0.0769 time to fit residues: 8.4045 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 : 0.228 ------------------------------------------------------------------------------- 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 132 THR 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 564 LEU 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 988 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.0050 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.076175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059475 restraints weight = 29805.881| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.26 r_work: 0.2942 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7683 Z= 0.105 Angle : 0.486 6.457 10461 Z= 0.247 Chirality : 0.035 0.166 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.332 79.360 1105 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.34 % Allowed : 15.86 % Favored : 81.79 % 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 aren not related in a simple way. whole: 2.24 (0.28), residues: 975 helix: 2.69 (0.21), residues: 625 sheet: -1.78 (0.61), residues: 65 loop : -0.49 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1138 TYR 0.005 0.001 TYR A 227 PHE 0.014 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 covalent geometry : bond 0.00236 ( 7682) covalent geometry : angle 0.48631 (10459) SS BOND : bond 0.00174 ( 1) SS BOND : angle 0.93045 ( 2) hydrogen bonds : bond 0.03122 ( 476) hydrogen bonds : angle 3.98900 ( 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 87 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7874 (tm-30) REVERT: A 135 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8887 (tm-30) REVERT: A 186 MET cc_start: 0.9219 (ptp) cc_final: 0.8830 (ptp) REVERT: A 669 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8535 (mm-40) REVERT: A 784 MET cc_start: 0.9119 (ttm) cc_final: 0.8818 (tmm) REVERT: A 1034 LEU cc_start: 0.9200 (mp) cc_final: 0.8667 (tt) REVERT: A 1051 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8038 (tm-30) outliers start: 17 outliers final: 15 residues processed: 80 average time/residue: 0.0717 time to fit residues: 8.3721 Evaluate side-chains 79 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 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 988 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1037 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.075496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059082 restraints weight = 29281.496| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 4.17 r_work: 0.2938 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7683 Z= 0.115 Angle : 0.512 9.542 10461 Z= 0.254 Chirality : 0.036 0.187 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.291 78.548 1105 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.62 % Allowed : 15.59 % Favored : 81.79 % 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 aren not related in a simple way. whole: 2.23 (0.28), residues: 975 helix: 2.64 (0.21), residues: 631 sheet: -1.34 (0.60), residues: 70 loop : -0.56 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1138 TYR 0.005 0.001 TYR A 227 PHE 0.013 0.001 PHE A 373 TRP 0.009 0.001 TRP A1124 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7682) covalent geometry : angle 0.51169 (10459) SS BOND : bond 0.00264 ( 1) SS BOND : angle 1.09400 ( 2) hydrogen bonds : bond 0.03168 ( 476) hydrogen bonds : angle 3.97509 ( 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 82 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7897 (tm-30) REVERT: A 135 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8907 (tm-30) REVERT: A 186 MET cc_start: 0.9205 (ptp) cc_final: 0.8797 (ptp) REVERT: A 430 MET cc_start: 0.9671 (tpp) cc_final: 0.9399 (mmm) REVERT: A 574 MET cc_start: 0.9495 (mmm) cc_final: 0.9279 (mmt) REVERT: A 629 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8157 (tm-30) REVERT: A 784 MET cc_start: 0.9124 (ttm) cc_final: 0.8824 (tmm) REVERT: A 1034 LEU cc_start: 0.9203 (mp) cc_final: 0.8661 (tt) REVERT: A 1051 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8029 (tm-30) outliers start: 19 outliers final: 16 residues processed: 75 average time/residue: 0.0675 time to fit residues: 7.7054 Evaluate side-chains 76 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 988 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1037 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.075227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058586 restraints weight = 29772.608| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.20 r_work: 0.2933 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7683 Z= 0.118 Angle : 0.520 9.461 10461 Z= 0.260 Chirality : 0.036 0.185 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.264 76.859 1105 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 15.72 % Favored : 81.79 % 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 aren not related in a simple way. whole: 2.17 (0.28), residues: 975 helix: 2.61 (0.21), residues: 631 sheet: -1.68 (0.63), residues: 65 loop : -0.55 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1138 TYR 0.006 0.001 TYR A 227 PHE 0.013 0.001 PHE A 373 TRP 0.010 0.001 TRP A1124 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7682) covalent geometry : angle 0.51946 (10459) SS BOND : bond 0.00273 ( 1) SS BOND : angle 1.10332 ( 2) hydrogen bonds : bond 0.03184 ( 476) hydrogen bonds : angle 3.99206 ( 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 78 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7896 (tm-30) REVERT: A 135 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8885 (tm-30) REVERT: A 186 MET cc_start: 0.9204 (ptp) cc_final: 0.8794 (ptp) REVERT: A 430 MET cc_start: 0.9670 (tpp) cc_final: 0.9395 (mmm) REVERT: A 629 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 784 MET cc_start: 0.9120 (ttm) cc_final: 0.8821 (tmm) REVERT: A 1051 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8005 (tm-30) outliers start: 18 outliers final: 17 residues processed: 71 average time/residue: 0.0602 time to fit residues: 6.4460 Evaluate side-chains 76 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 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 988 MET Chi-restraints excluded: chain A residue 1028 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.0050 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.073264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056933 restraints weight = 29697.057| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.01 r_work: 0.2913 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7683 Z= 0.152 Angle : 0.532 9.417 10461 Z= 0.268 Chirality : 0.037 0.223 1206 Planarity : 0.004 0.039 1315 Dihedral : 5.276 75.247 1105 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.21 % Allowed : 16.14 % 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 aren not related in a simple way. whole: 2.17 (0.28), residues: 975 helix: 2.62 (0.21), residues: 630 sheet: -1.68 (0.63), residues: 65 loop : -0.58 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1138 TYR 0.007 0.001 TYR A 227 PHE 0.013 0.001 PHE A 373 TRP 0.010 0.001 TRP A 680 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7682) covalent geometry : angle 0.53131 (10459) SS BOND : bond 0.00370 ( 1) SS BOND : angle 1.39522 ( 2) hydrogen bonds : bond 0.03355 ( 476) hydrogen bonds : angle 4.06881 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1860.83 seconds wall clock time: 32 minutes 32.79 seconds (1952.79 seconds total)