Starting phenix.real_space_refine on Wed Sep 17 09:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8x_44361/09_2025/9b8x_44361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8x_44361/09_2025/9b8x_44361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b8x_44361/09_2025/9b8x_44361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8x_44361/09_2025/9b8x_44361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b8x_44361/09_2025/9b8x_44361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8x_44361/09_2025/9b8x_44361.map" } resolution = 3.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 38 5.16 5 C 4898 2.51 5 N 1336 2.21 5 O 1290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 7564 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7562 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASP:plan': 15, 'HIS:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 217 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.93, per 1000 atoms: 0.26 Number of scatterers: 7564 At special positions: 0 Unit cell: (86.112, 120.888, 151.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 38 16.00 O 1290 8.00 N 1336 7.00 C 4898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 37 " distance=2.04 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.03 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: 0.68 Conformation dependent library (CDL) restraints added in 429.4 milliseconds Enol-peptide restraints added in 476.8 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: 49 helices and 5 sheets defined 67.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.823A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.922A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (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: 3.699A 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 325 through 336 removed outlier: 3.569A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.992A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' 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: 4.429A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.736A 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: 3.956A 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 581 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 removed outlier: 3.594A pdb=" N ARG A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.696A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 767 through 778 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 861 Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 906 removed outlier: 3.670A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 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 975 removed outlier: 4.992A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.541A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.520A pdb=" N MET A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.733A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1050 through 1071 removed outlier: 4.135A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.156A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1177 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 3.558A pdb=" N THR A 68 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.453A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.288A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 removed outlier: 7.989A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1000 through 1001 469 hydrogen bonds defined for protein. 1377 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: 1.26 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2457 1.35 - 1.47: 1887 1.47 - 1.59: 3336 1.59 - 1.71: 0 1.71 - 1.83: 57 Bond restraints: 7737 Sorted by residual: bond pdb=" C PHE A 207 " pdb=" N PRO A 208 " ideal model delta sigma weight residual 1.335 1.343 -0.008 8.70e-03 1.32e+04 8.78e-01 bond pdb=" N PRO A 40 " pdb=" CA PRO A 40 " ideal model delta sigma weight residual 1.466 1.473 -0.008 1.21e-02 6.83e+03 4.14e-01 bond pdb=" CB CYS A 37 " pdb=" SG CYS A 37 " ideal model delta sigma weight residual 1.808 1.828 -0.020 3.30e-02 9.18e+02 3.80e-01 bond pdb=" CA PRO A1003 " pdb=" C PRO A1003 " ideal model delta sigma weight residual 1.517 1.513 0.004 6.70e-03 2.23e+04 3.54e-01 bond pdb=" C PRO A 700 " pdb=" N PRO A 701 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.19e-02 7.06e+03 3.46e-01 ... (remaining 7732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 10346 1.26 - 2.52: 132 2.52 - 3.78: 33 3.78 - 5.04: 8 5.04 - 6.30: 2 Bond angle restraints: 10521 Sorted by residual: angle pdb=" C ARG A 334 " pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 122.66 120.38 2.28 9.70e-01 1.06e+00 5.54e+00 angle pdb=" C GLY A 263 " pdb=" N VAL A 264 " pdb=" CA VAL A 264 " ideal model delta sigma weight residual 121.97 125.86 -3.89 1.80e+00 3.09e-01 4.68e+00 angle pdb=" N PRO A1077 " pdb=" CA PRO A1077 " pdb=" C PRO A1077 " ideal model delta sigma weight residual 110.70 113.24 -2.54 1.22e+00 6.72e-01 4.33e+00 angle pdb=" CA VAL A 221 " pdb=" C VAL A 221 " pdb=" N GLN A 222 " ideal model delta sigma weight residual 116.60 119.42 -2.82 1.45e+00 4.76e-01 3.79e+00 angle pdb=" N PRO A 700 " pdb=" CA PRO A 700 " pdb=" C PRO A 700 " ideal model delta sigma weight residual 110.70 113.02 -2.32 1.22e+00 6.72e-01 3.62e+00 ... (remaining 10516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.64: 4182 11.64 - 23.29: 259 23.29 - 34.93: 73 34.93 - 46.57: 29 46.57 - 58.21: 6 Dihedral angle restraints: 4549 sinusoidal: 1701 harmonic: 2848 Sorted by residual: 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 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA CYS A 35 " pdb=" C CYS A 35 " pdb=" N GLN A 36 " pdb=" CA GLN A 36 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" SG CYS A 35 " pdb=" CB CYS A 37 " pdb=" SG CYS A 37 " pdb=" CA CYS A 37 " ideal model delta sinusoidal sigma weight residual 79.00 24.86 54.14 1 2.00e+01 2.50e-03 9.94e+00 ... (remaining 4546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 761 0.026 - 0.051: 286 0.051 - 0.077: 107 0.077 - 0.102: 40 0.102 - 0.128: 12 Chirality restraints: 1206 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE A 278 " pdb=" N ILE A 278 " pdb=" C ILE A 278 " pdb=" CB ILE A 278 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CB VAL A 264 " pdb=" CA VAL A 264 " pdb=" CG1 VAL A 264 " pdb=" CG2 VAL A 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 1203 not shown) Planarity restraints: 1329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1076 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A1077 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 700 " 0.024 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 701 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 701 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 701 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 917 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 918 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 918 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 918 " 0.019 5.00e-02 4.00e+02 ... (remaining 1326 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2430 2.84 - 3.36: 7621 3.36 - 3.87: 12543 3.87 - 4.39: 13550 4.39 - 4.90: 23861 Nonbonded interactions: 60005 Sorted by model distance: nonbonded pdb=" O PHE A 454 " pdb=" NH1 ARG A 459 " model vdw 2.325 3.120 nonbonded pdb=" OH TYR A 75 " pdb=" O PRO A 203 " model vdw 2.335 3.040 nonbonded pdb=" OD1 ASP A 431 " pdb=" ND2 ASN A 435 " model vdw 2.343 3.120 nonbonded pdb=" O ILE A 974 " pdb=" ND2 ASN A1032 " model vdw 2.354 3.120 nonbonded pdb=" O PHE A 667 " pdb=" NE2 GLN A 673 " model vdw 2.370 3.120 ... (remaining 60000 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: 3.760 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.002 0.028 7739 Z= 0.100 Angle : 0.418 6.301 10525 Z= 0.226 Chirality : 0.034 0.128 1206 Planarity : 0.004 0.041 1329 Dihedral : 9.222 58.212 2703 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.40 % Allowed : 4.71 % Favored : 94.89 % 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: 2.41 (0.28), residues: 975 helix: 2.78 (0.21), residues: 605 sheet: -1.14 (0.71), residues: 59 loop : -0.25 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 905 TYR 0.007 0.001 TYR A 968 PHE 0.007 0.001 PHE A 627 TRP 0.010 0.001 TRP A1124 HIS 0.002 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 7737) covalent geometry : angle 0.41684 (10521) SS BOND : bond 0.00330 ( 2) SS BOND : angle 1.66858 ( 4) hydrogen bonds : bond 0.11359 ( 469) hydrogen bonds : angle 4.48451 ( 1377) *********************** 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 76 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8314 (m170) cc_final: 0.7984 (m170) REVERT: A 235 VAL cc_start: 0.8259 (t) cc_final: 0.7994 (m) REVERT: A 784 MET cc_start: 0.8223 (tpt) cc_final: 0.7732 (ttt) REVERT: A 995 SER cc_start: 0.9457 (p) cc_final: 0.9230 (t) REVERT: A 1054 SER cc_start: 0.9479 (m) cc_final: 0.9224 (p) REVERT: A 1166 ARG cc_start: 0.6677 (tpt90) cc_final: 0.5994 (mmp-170) outliers start: 3 outliers final: 2 residues processed: 76 average time/residue: 0.7149 time to fit residues: 57.0173 Evaluate side-chains 40 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 44 HIS A 228 ASN A 240 HIS A 980 GLN A1007 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.056980 restraints weight = 23322.411| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.21 r_work: 0.2859 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7739 Z= 0.233 Angle : 0.567 7.489 10525 Z= 0.290 Chirality : 0.039 0.139 1206 Planarity : 0.005 0.074 1329 Dihedral : 3.872 43.684 1079 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.48 % Allowed : 8.21 % Favored : 90.31 % 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: 2.18 (0.28), residues: 975 helix: 2.51 (0.21), residues: 610 sheet: -1.34 (0.68), residues: 59 loop : -0.16 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 108 TYR 0.009 0.001 TYR A 790 PHE 0.012 0.002 PHE A 667 TRP 0.011 0.001 TRP A1124 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 7737) covalent geometry : angle 0.56587 (10521) SS BOND : bond 0.00399 ( 2) SS BOND : angle 2.25065 ( 4) hydrogen bonds : bond 0.03971 ( 469) hydrogen bonds : angle 4.02243 ( 1377) *********************** 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 50 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8402 (m170) cc_final: 0.8055 (m170) REVERT: A 235 VAL cc_start: 0.8653 (t) cc_final: 0.8350 (m) REVERT: A 784 MET cc_start: 0.8009 (tpt) cc_final: 0.7553 (ttt) REVERT: A 857 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8142 (mtm110) REVERT: A 1054 SER cc_start: 0.9475 (m) cc_final: 0.9261 (p) REVERT: A 1166 ARG cc_start: 0.6697 (tpt90) cc_final: 0.5809 (mmp-170) outliers start: 11 outliers final: 3 residues processed: 48 average time/residue: 0.7049 time to fit residues: 35.7450 Evaluate side-chains 40 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 857 ARG Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 85 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.080538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058267 restraints weight = 23130.584| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.22 r_work: 0.2893 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7739 Z= 0.105 Angle : 0.445 7.924 10525 Z= 0.229 Chirality : 0.035 0.135 1206 Planarity : 0.004 0.046 1329 Dihedral : 3.284 17.261 1075 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.02 % Allowed : 9.02 % Favored : 88.96 % 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: 2.37 (0.28), residues: 975 helix: 2.66 (0.21), residues: 611 sheet: -1.37 (0.68), residues: 59 loop : -0.07 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 108 TYR 0.005 0.001 TYR A 968 PHE 0.008 0.001 PHE A 627 TRP 0.010 0.001 TRP A1124 HIS 0.002 0.000 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7737) covalent geometry : angle 0.44273 (10521) SS BOND : bond 0.00366 ( 2) SS BOND : angle 2.22587 ( 4) hydrogen bonds : bond 0.03287 ( 469) hydrogen bonds : angle 3.82567 ( 1377) *********************** 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 52 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8461 (m170) cc_final: 0.8111 (m170) REVERT: A 235 VAL cc_start: 0.8679 (t) cc_final: 0.8364 (m) REVERT: A 595 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8896 (tt) REVERT: A 784 MET cc_start: 0.8015 (tpt) cc_final: 0.7566 (ttt) REVERT: A 995 SER cc_start: 0.9405 (p) cc_final: 0.9174 (t) REVERT: A 1166 ARG cc_start: 0.6533 (tpt90) cc_final: 0.5714 (mmp-170) outliers start: 15 outliers final: 5 residues processed: 51 average time/residue: 0.6249 time to fit residues: 33.8870 Evaluate side-chains 41 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 59 optimal weight: 0.0470 chunk 66 optimal weight: 0.0370 chunk 31 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.080442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.058174 restraints weight = 23443.386| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.22 r_work: 0.2891 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7739 Z= 0.103 Angle : 0.445 7.971 10525 Z= 0.226 Chirality : 0.035 0.138 1206 Planarity : 0.004 0.046 1329 Dihedral : 3.240 16.868 1075 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.75 % Allowed : 10.09 % Favored : 88.16 % 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: 2.43 (0.28), residues: 975 helix: 2.71 (0.21), residues: 611 sheet: -0.96 (0.63), residues: 69 loop : -0.09 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 327 TYR 0.005 0.001 TYR A 256 PHE 0.008 0.001 PHE A 627 TRP 0.009 0.001 TRP A1124 HIS 0.002 0.000 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7737) covalent geometry : angle 0.44280 (10521) SS BOND : bond 0.00324 ( 2) SS BOND : angle 2.20619 ( 4) hydrogen bonds : bond 0.03129 ( 469) hydrogen bonds : angle 3.74923 ( 1377) *********************** 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 50 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8503 (m170) cc_final: 0.8159 (m170) REVERT: A 235 VAL cc_start: 0.8756 (t) cc_final: 0.8460 (m) REVERT: A 576 MET cc_start: 0.8982 (tpp) cc_final: 0.8605 (mmm) REVERT: A 595 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8908 (tt) REVERT: A 601 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8104 (ptp-110) REVERT: A 784 MET cc_start: 0.7964 (tpt) cc_final: 0.7546 (ttt) REVERT: A 995 SER cc_start: 0.9407 (p) cc_final: 0.9170 (t) REVERT: A 1166 ARG cc_start: 0.6612 (tpt90) cc_final: 0.5716 (mmp-170) outliers start: 13 outliers final: 6 residues processed: 49 average time/residue: 0.6021 time to fit residues: 31.4289 Evaluate side-chains 44 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.078712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056321 restraints weight = 23337.690| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.21 r_work: 0.2844 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7739 Z= 0.176 Angle : 0.487 7.586 10525 Z= 0.247 Chirality : 0.037 0.140 1206 Planarity : 0.004 0.048 1329 Dihedral : 3.303 17.995 1075 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.48 % Allowed : 11.31 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.65 (0.21), residues: 611 sheet: -1.45 (0.68), residues: 59 loop : -0.18 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.006 0.001 TYR A1015 PHE 0.011 0.001 PHE A 627 TRP 0.008 0.001 TRP A1124 HIS 0.011 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7737) covalent geometry : angle 0.48524 (10521) SS BOND : bond 0.00256 ( 2) SS BOND : angle 2.02339 ( 4) hydrogen bonds : bond 0.03462 ( 469) hydrogen bonds : angle 3.81964 ( 1377) *********************** 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 44 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8501 (m170) cc_final: 0.8161 (m170) REVERT: A 576 MET cc_start: 0.9036 (tpp) cc_final: 0.8685 (mmm) REVERT: A 601 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7935 (ptp-110) REVERT: A 784 MET cc_start: 0.7957 (tpt) cc_final: 0.7546 (ttt) outliers start: 11 outliers final: 4 residues processed: 43 average time/residue: 0.5817 time to fit residues: 26.8383 Evaluate side-chains 38 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.078861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056570 restraints weight = 23250.082| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.20 r_work: 0.2850 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7739 Z= 0.128 Angle : 0.466 8.815 10525 Z= 0.234 Chirality : 0.036 0.137 1206 Planarity : 0.004 0.047 1329 Dihedral : 3.291 17.534 1075 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.75 % Allowed : 11.31 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.28), residues: 975 helix: 2.69 (0.21), residues: 610 sheet: -1.01 (0.63), residues: 69 loop : -0.12 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.005 0.001 TYR A 256 PHE 0.009 0.001 PHE A 627 TRP 0.008 0.001 TRP A1124 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7737) covalent geometry : angle 0.46373 (10521) SS BOND : bond 0.00278 ( 2) SS BOND : angle 2.15262 ( 4) hydrogen bonds : bond 0.03280 ( 469) hydrogen bonds : angle 3.79935 ( 1377) *********************** 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 48 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8519 (m170) cc_final: 0.8170 (m170) REVERT: A 186 MET cc_start: 0.9155 (mtp) cc_final: 0.8889 (mtm) REVERT: A 576 MET cc_start: 0.9036 (tpp) cc_final: 0.8718 (mmm) REVERT: A 601 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8091 (ptp-110) REVERT: A 784 MET cc_start: 0.7942 (tpt) cc_final: 0.7541 (ttt) outliers start: 13 outliers final: 4 residues processed: 46 average time/residue: 0.6016 time to fit residues: 29.4857 Evaluate side-chains 40 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.078987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056763 restraints weight = 23191.375| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.20 r_work: 0.2855 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7739 Z= 0.112 Angle : 0.461 8.625 10525 Z= 0.230 Chirality : 0.036 0.136 1206 Planarity : 0.004 0.047 1329 Dihedral : 3.250 17.244 1075 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.48 % Allowed : 11.84 % Favored : 86.68 % 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: 2.44 (0.28), residues: 975 helix: 2.73 (0.21), residues: 610 sheet: -0.93 (0.65), residues: 69 loop : -0.11 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 459 TYR 0.005 0.001 TYR A 256 PHE 0.009 0.001 PHE A 627 TRP 0.009 0.001 TRP A 772 HIS 0.002 0.000 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7737) covalent geometry : angle 0.45933 (10521) SS BOND : bond 0.00275 ( 2) SS BOND : angle 2.16868 ( 4) hydrogen bonds : bond 0.03105 ( 469) hydrogen bonds : angle 3.74916 ( 1377) *********************** 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 50 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8590 (m170) cc_final: 0.8211 (m170) REVERT: A 576 MET cc_start: 0.9055 (tpp) cc_final: 0.8726 (mmm) REVERT: A 601 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8094 (ptp-110) REVERT: A 784 MET cc_start: 0.7946 (tpt) cc_final: 0.7556 (ttt) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.5444 time to fit residues: 28.6348 Evaluate side-chains 39 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.077166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054747 restraints weight = 23521.950| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.21 r_work: 0.2808 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7739 Z= 0.187 Angle : 0.524 11.345 10525 Z= 0.264 Chirality : 0.038 0.146 1206 Planarity : 0.004 0.049 1329 Dihedral : 3.385 18.929 1075 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.21 % Allowed : 12.25 % Favored : 86.54 % 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: 2.25 (0.28), residues: 975 helix: 2.59 (0.21), residues: 610 sheet: -1.42 (0.72), residues: 58 loop : -0.17 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.007 0.001 TYR A1015 PHE 0.012 0.001 PHE A 627 TRP 0.010 0.001 TRP A 213 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 7737) covalent geometry : angle 0.52302 (10521) SS BOND : bond 0.00264 ( 2) SS BOND : angle 2.07287 ( 4) hydrogen bonds : bond 0.03713 ( 469) hydrogen bonds : angle 3.90890 ( 1377) *********************** 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 44 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8861 (ptpt) cc_final: 0.8461 (pptt) REVERT: A 66 HIS cc_start: 0.8571 (m170) cc_final: 0.8185 (m170) REVERT: A 601 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7913 (ptp-110) REVERT: A 784 MET cc_start: 0.7925 (tpt) cc_final: 0.7533 (ttt) outliers start: 9 outliers final: 4 residues processed: 42 average time/residue: 0.6339 time to fit residues: 28.3421 Evaluate side-chains 39 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.078137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055945 restraints weight = 23192.076| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.19 r_work: 0.2834 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7739 Z= 0.121 Angle : 0.473 8.036 10525 Z= 0.238 Chirality : 0.036 0.135 1206 Planarity : 0.004 0.048 1329 Dihedral : 3.332 17.978 1075 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.21 % Allowed : 12.38 % Favored : 86.41 % 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: 2.29 (0.28), residues: 975 helix: 2.58 (0.21), residues: 616 sheet: -1.55 (0.71), residues: 59 loop : -0.05 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.005 0.001 TYR A 256 PHE 0.009 0.001 PHE A 627 TRP 0.010 0.001 TRP A 772 HIS 0.003 0.000 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7737) covalent geometry : angle 0.47175 (10521) SS BOND : bond 0.00248 ( 2) SS BOND : angle 2.13119 ( 4) hydrogen bonds : bond 0.03259 ( 469) hydrogen bonds : angle 3.83791 ( 1377) *********************** 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 44 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8909 (ptpt) cc_final: 0.8707 (pptt) REVERT: A 66 HIS cc_start: 0.8642 (m170) cc_final: 0.8241 (m170) REVERT: A 576 MET cc_start: 0.9088 (tpp) cc_final: 0.8702 (mmm) REVERT: A 601 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7896 (ptp-110) REVERT: A 784 MET cc_start: 0.7927 (tpt) cc_final: 0.7549 (ttt) outliers start: 9 outliers final: 4 residues processed: 42 average time/residue: 0.6018 time to fit residues: 26.8465 Evaluate side-chains 40 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.077012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.054606 restraints weight = 23258.995| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.20 r_work: 0.2806 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7739 Z= 0.181 Angle : 0.512 11.209 10525 Z= 0.258 Chirality : 0.038 0.143 1206 Planarity : 0.004 0.048 1329 Dihedral : 3.396 19.110 1075 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.08 % Allowed : 12.65 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.28), residues: 975 helix: 2.50 (0.21), residues: 616 sheet: -1.50 (0.71), residues: 58 loop : -0.13 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.006 0.001 TYR A 464 PHE 0.011 0.001 PHE A 899 TRP 0.010 0.001 TRP A 213 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7737) covalent geometry : angle 0.51078 (10521) SS BOND : bond 0.00264 ( 2) SS BOND : angle 2.07434 ( 4) hydrogen bonds : bond 0.03605 ( 469) hydrogen bonds : angle 3.90175 ( 1377) ********************** 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 41 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8952 (ptpt) cc_final: 0.8740 (pptt) REVERT: A 576 MET cc_start: 0.9066 (tpp) cc_final: 0.8736 (mmm) REVERT: A 601 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7894 (ptp-110) REVERT: A 784 MET cc_start: 0.7923 (tpt) cc_final: 0.7544 (ttt) outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 0.6943 time to fit residues: 29.3552 Evaluate side-chains 37 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 chunk 90 optimal weight: 0.5980 chunk 61 optimal weight: 0.0020 overall best weight: 0.4086 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.078648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.056629 restraints weight = 23062.999| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.18 r_work: 0.2856 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7739 Z= 0.096 Angle : 0.467 8.364 10525 Z= 0.233 Chirality : 0.036 0.133 1206 Planarity : 0.004 0.052 1329 Dihedral : 3.325 16.998 1075 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.27 % Allowed : 13.46 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.28), residues: 975 helix: 2.61 (0.21), residues: 616 sheet: -1.49 (0.71), residues: 58 loop : -0.03 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 327 TYR 0.005 0.001 TYR A 968 PHE 0.008 0.001 PHE A 627 TRP 0.011 0.001 TRP A 772 HIS 0.002 0.000 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 7737) covalent geometry : angle 0.46490 (10521) SS BOND : bond 0.00265 ( 2) SS BOND : angle 2.16913 ( 4) hydrogen bonds : bond 0.03057 ( 469) hydrogen bonds : angle 3.78746 ( 1377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2494.18 seconds wall clock time: 43 minutes 24.19 seconds (2604.19 seconds total)