Starting phenix.real_space_refine on Tue Jan 14 23:52:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8x_44361/01_2025/9b8x_44361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8x_44361/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8x_44361/01_2025/9b8x_44361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8x_44361/01_2025/9b8x_44361.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8x_44361/01_2025/9b8x_44361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8x_44361/01_2025/9b8x_44361.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 4, 'ASP:plan': 15, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 12} 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: 5.40, per 1000 atoms: 0.71 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: 1.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.85 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: 2.51 Time building geometry restraints manager: 2.18 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: 17.290 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.490 ------------------------------------------------------------------------------- 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 7737 Z= 0.129 Angle : 0.417 6.301 10521 Z= 0.225 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (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 TRP 0.010 0.001 TRP A1124 HIS 0.002 0.001 HIS A1002 PHE 0.007 0.001 PHE A 627 TYR 0.007 0.001 TYR A 968 ARG 0.002 0.000 ARG A 905 *********************** 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 : 0.835 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: 1.4423 time to fit residues: 115.9437 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 : 0.921 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 240 HIS A 980 GLN A1007 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.082063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059848 restraints weight = 23180.184| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.23 r_work: 0.2934 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7737 Z= 0.221 Angle : 0.496 8.204 10521 Z= 0.253 Chirality : 0.036 0.156 1206 Planarity : 0.005 0.073 1329 Dihedral : 3.718 42.573 1079 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.75 % Allowed : 7.67 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.28), residues: 975 helix: 2.67 (0.21), residues: 610 sheet: -1.24 (0.69), residues: 59 loop : -0.10 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1124 HIS 0.003 0.001 HIS A 240 PHE 0.011 0.001 PHE A 667 TYR 0.006 0.001 TYR A 75 ARG 0.013 0.001 ARG A 108 *********************** 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 53 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8409 (m170) cc_final: 0.8046 (m170) REVERT: A 235 VAL cc_start: 0.8591 (t) cc_final: 0.8281 (m) REVERT: A 595 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8806 (tt) REVERT: A 784 MET cc_start: 0.8170 (tpt) cc_final: 0.7691 (ttt) REVERT: A 995 SER cc_start: 0.9405 (p) cc_final: 0.9174 (t) REVERT: A 1054 SER cc_start: 0.9493 (m) cc_final: 0.9287 (p) REVERT: A 1166 ARG cc_start: 0.6583 (tpt90) cc_final: 0.5920 (mmp-170) outliers start: 13 outliers final: 6 residues processed: 50 average time/residue: 1.2505 time to fit residues: 67.0030 Evaluate side-chains 44 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 200 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.078764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056159 restraints weight = 23563.555| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.24 r_work: 0.2835 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7737 Z= 0.262 Angle : 0.491 7.676 10521 Z= 0.253 Chirality : 0.037 0.137 1206 Planarity : 0.004 0.048 1329 Dihedral : 3.370 18.674 1075 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.15 % Allowed : 9.42 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.28), residues: 975 helix: 2.61 (0.21), residues: 610 sheet: -1.43 (0.68), residues: 59 loop : -0.12 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.004 0.001 HIS A1128 PHE 0.010 0.001 PHE A 627 TYR 0.008 0.001 TYR A 256 ARG 0.008 0.000 ARG A 327 *********************** 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 51 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8439 (m170) cc_final: 0.8106 (m170) REVERT: A 576 MET cc_start: 0.8974 (tpp) cc_final: 0.8614 (mmm) REVERT: A 622 MET cc_start: 0.8988 (mtm) cc_final: 0.8565 (mtm) REVERT: A 784 MET cc_start: 0.7950 (tpt) cc_final: 0.7558 (ttt) REVERT: A 857 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7822 (mtm-85) REVERT: A 1166 ARG cc_start: 0.6687 (tpt90) cc_final: 0.5606 (mmp-170) outliers start: 16 outliers final: 5 residues processed: 49 average time/residue: 1.3522 time to fit residues: 70.6244 Evaluate side-chains 38 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 695 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.078118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.055740 restraints weight = 23193.430| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.20 r_work: 0.2831 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7737 Z= 0.250 Angle : 0.479 8.198 10521 Z= 0.245 Chirality : 0.037 0.137 1206 Planarity : 0.004 0.049 1329 Dihedral : 3.379 18.166 1075 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.02 % Allowed : 10.63 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.28), residues: 975 helix: 2.61 (0.21), residues: 611 sheet: -1.04 (0.63), residues: 69 loop : -0.15 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 776 HIS 0.004 0.001 HIS A1128 PHE 0.010 0.001 PHE A 899 TYR 0.005 0.001 TYR A 256 ARG 0.019 0.001 ARG A 327 *********************** 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 48 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8497 (m170) cc_final: 0.8162 (m170) REVERT: A 576 MET cc_start: 0.9004 (tpp) cc_final: 0.8757 (tpp) REVERT: A 601 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7903 (ptp-110) REVERT: A 622 MET cc_start: 0.9023 (mtm) cc_final: 0.8720 (mtm) REVERT: A 784 MET cc_start: 0.7945 (tpt) cc_final: 0.7537 (ttt) outliers start: 15 outliers final: 7 residues processed: 46 average time/residue: 1.1762 time to fit residues: 58.1805 Evaluate side-chains 39 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 200 LEU Chi-restraints excluded: chain A residue 240 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 0.0030 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.079271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056982 restraints weight = 22939.126| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.19 r_work: 0.2862 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7737 Z= 0.140 Angle : 0.455 8.853 10521 Z= 0.227 Chirality : 0.035 0.138 1206 Planarity : 0.004 0.047 1329 Dihedral : 3.317 17.906 1075 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.35 % Allowed : 11.17 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.28), residues: 975 helix: 2.72 (0.21), residues: 610 sheet: -0.99 (0.63), residues: 69 loop : -0.19 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 772 HIS 0.004 0.000 HIS A 240 PHE 0.008 0.001 PHE A 627 TYR 0.005 0.001 TYR A 256 ARG 0.005 0.000 ARG A 108 *********************** 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 43 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8517 (m170) cc_final: 0.8169 (m170) REVERT: A 576 MET cc_start: 0.8983 (tpp) cc_final: 0.8721 (tpp) REVERT: A 601 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7856 (ptp-110) REVERT: A 622 MET cc_start: 0.9011 (mtm) cc_final: 0.8698 (mtm) REVERT: A 784 MET cc_start: 0.7947 (tpt) cc_final: 0.7565 (ttt) outliers start: 10 outliers final: 5 residues processed: 42 average time/residue: 1.3113 time to fit residues: 59.0370 Evaluate side-chains 37 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.078029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055667 restraints weight = 23248.995| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.20 r_work: 0.2830 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7737 Z= 0.225 Angle : 0.477 7.772 10521 Z= 0.238 Chirality : 0.036 0.141 1206 Planarity : 0.004 0.049 1329 Dihedral : 3.309 18.213 1075 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.21 % Allowed : 11.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.28), residues: 975 helix: 2.69 (0.21), residues: 610 sheet: -1.42 (0.70), residues: 59 loop : -0.11 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 680 HIS 0.003 0.001 HIS A1128 PHE 0.010 0.001 PHE A 627 TYR 0.007 0.001 TYR A1015 ARG 0.004 0.000 ARG A 108 *********************** 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 44 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8548 (m170) cc_final: 0.8195 (m170) REVERT: A 576 MET cc_start: 0.9015 (tpp) cc_final: 0.8803 (tpp) REVERT: A 601 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7845 (ptp-110) REVERT: A 622 MET cc_start: 0.9038 (mtm) cc_final: 0.8808 (mtp) REVERT: A 784 MET cc_start: 0.7941 (tpt) cc_final: 0.7541 (ttt) outliers start: 9 outliers final: 3 residues processed: 43 average time/residue: 1.1677 time to fit residues: 54.4548 Evaluate side-chains 36 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.078691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056441 restraints weight = 22794.523| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.17 r_work: 0.2849 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7737 Z= 0.154 Angle : 0.457 11.864 10521 Z= 0.225 Chirality : 0.035 0.138 1206 Planarity : 0.004 0.048 1329 Dihedral : 3.262 17.531 1075 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.88 % Allowed : 11.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.28), residues: 975 helix: 2.77 (0.21), residues: 610 sheet: -1.50 (0.68), residues: 59 loop : -0.11 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 772 HIS 0.002 0.000 HIS A1128 PHE 0.008 0.001 PHE A 627 TYR 0.005 0.001 TYR A 256 ARG 0.003 0.000 ARG A 108 *********************** 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 49 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9217 (mptp) cc_final: 0.9004 (ptpt) REVERT: A 66 HIS cc_start: 0.8599 (m170) cc_final: 0.8222 (m170) REVERT: A 576 MET cc_start: 0.8987 (tpp) cc_final: 0.8698 (tpp) REVERT: A 601 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7835 (ptp-110) REVERT: A 622 MET cc_start: 0.9024 (mtm) cc_final: 0.8681 (mtm) REVERT: A 784 MET cc_start: 0.7938 (tpt) cc_final: 0.7549 (ttt) outliers start: 14 outliers final: 4 residues processed: 47 average time/residue: 1.1499 time to fit residues: 58.4243 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 : 1.102 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.075195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.052784 restraints weight = 23555.471| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.18 r_work: 0.2757 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7737 Z= 0.451 Angle : 0.602 6.811 10521 Z= 0.302 Chirality : 0.040 0.138 1206 Planarity : 0.005 0.051 1329 Dihedral : 3.539 20.961 1075 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.21 % Allowed : 11.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.28), residues: 975 helix: 2.51 (0.21), residues: 608 sheet: -1.62 (0.69), residues: 58 loop : -0.28 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 649 HIS 0.007 0.001 HIS A1128 PHE 0.014 0.002 PHE A 627 TYR 0.011 0.001 TYR A 464 ARG 0.004 0.001 ARG A 197 *********************** 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 41 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9220 (mptp) cc_final: 0.8992 (ptpt) REVERT: A 601 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7876 (ptp-110) REVERT: A 622 MET cc_start: 0.9094 (mtm) cc_final: 0.8884 (mtp) REVERT: A 784 MET cc_start: 0.7922 (tpt) cc_final: 0.7524 (ttt) outliers start: 9 outliers final: 4 residues processed: 40 average time/residue: 1.3617 time to fit residues: 58.3877 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 : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 872 LEU 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 97 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.0060 chunk 82 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.077548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.055247 restraints weight = 23287.253| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.19 r_work: 0.2820 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7737 Z= 0.154 Angle : 0.474 11.179 10521 Z= 0.235 Chirality : 0.036 0.135 1206 Planarity : 0.004 0.049 1329 Dihedral : 3.397 18.551 1075 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.21 % Allowed : 11.71 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.28), residues: 975 helix: 2.63 (0.21), residues: 610 sheet: -1.55 (0.70), residues: 58 loop : -0.13 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 772 HIS 0.003 0.000 HIS A1128 PHE 0.009 0.001 PHE A 627 TYR 0.005 0.001 TYR A 968 ARG 0.003 0.000 ARG A 108 *********************** 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 43 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9223 (mptp) cc_final: 0.9003 (ptpt) REVERT: A 601 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7851 (ptp-110) REVERT: A 784 MET cc_start: 0.7876 (tpt) cc_final: 0.7514 (ttt) outliers start: 9 outliers final: 1 residues processed: 43 average time/residue: 1.4912 time to fit residues: 68.4664 Evaluate side-chains 34 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 ARG 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 32 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 82 optimal weight: 0.0070 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.078562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056528 restraints weight = 23196.458| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.19 r_work: 0.2852 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7737 Z= 0.138 Angle : 0.456 7.871 10521 Z= 0.226 Chirality : 0.035 0.138 1206 Planarity : 0.004 0.049 1329 Dihedral : 3.247 17.438 1075 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.40 % Allowed : 12.79 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.28), residues: 975 helix: 2.74 (0.21), residues: 610 sheet: -1.62 (0.69), residues: 59 loop : -0.08 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 772 HIS 0.002 0.000 HIS A1128 PHE 0.007 0.001 PHE A 627 TYR 0.005 0.001 TYR A 968 ARG 0.003 0.000 ARG A 108 ********************** 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 39 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9228 (mptp) cc_final: 0.8997 (ptpt) REVERT: A 576 MET cc_start: 0.9008 (tpp) cc_final: 0.8606 (mmm) REVERT: A 601 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7828 (ptp-110) REVERT: A 784 MET cc_start: 0.7926 (tpt) cc_final: 0.7545 (ttt) outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 1.4578 time to fit residues: 60.5524 Evaluate side-chains 35 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 ARG 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 3 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 9 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 72 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- 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 = 0.078713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056738 restraints weight = 22921.139| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.17 r_work: 0.2860 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7737 Z= 0.134 Angle : 0.464 11.255 10521 Z= 0.228 Chirality : 0.035 0.137 1206 Planarity : 0.004 0.083 1329 Dihedral : 3.222 16.526 1075 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.40 % Allowed : 13.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.28), residues: 975 helix: 2.78 (0.21), residues: 610 sheet: -1.64 (0.69), residues: 59 loop : -0.04 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 772 HIS 0.002 0.000 HIS A1128 PHE 0.008 0.001 PHE A 627 TYR 0.004 0.001 TYR A 859 ARG 0.010 0.000 ARG A 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4956.53 seconds wall clock time: 89 minutes 16.22 seconds (5356.22 seconds total)