Starting phenix.real_space_refine on Tue Sep 24 02:10:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/09_2024/8bv5_16255.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/09_2024/8bv5_16255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/09_2024/8bv5_16255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/09_2024/8bv5_16255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/09_2024/8bv5_16255.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/09_2024/8bv5_16255.cif" } resolution = 3.54 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 3971 2.51 5 N 1107 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6296 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3518 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 9, 'TRANS': 427} Chain breaks: 4 Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2716 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'FOK': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.54, per 1000 atoms: 0.88 Number of scatterers: 6296 At special positions: 0 Unit cell: (112.2, 97.02, 82.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 3 15.00 Mg 1 11.99 O 1179 8.00 N 1107 7.00 C 3971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 469 " 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: 1.75 Conformation dependent library (CDL) restraints added in 947.3 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 51.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 361 through 378 Processing helix chain 'A' and resid 381 through 393 removed outlier: 4.209A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.549A pdb=" N HIS A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 500 Processing helix chain 'A' and resid 533 through 546 removed outlier: 3.734A pdb=" N ASP A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.666A pdb=" N LEU A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 Processing helix chain 'A' and resid 958 through 967 removed outlier: 3.769A pdb=" N GLU A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 1006 through 1025 Processing helix chain 'A' and resid 1059 through 1083 Processing helix chain 'A' and resid 1114 through 1126 removed outlier: 3.692A pdb=" N ASN A1118 " --> pdb=" O GLY A1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 89 through 113 removed outlier: 3.907A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.679A pdb=" N ASN B 254 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 312 through 318 removed outlier: 3.994A pdb=" N ALA B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 352 Processing helix chain 'B' and resid 369 through 388 removed outlier: 3.941A pdb=" N LEU B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 417 removed outlier: 5.730A pdb=" N ARG A 411 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS A 519 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLU A 413 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 517 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 463 removed outlier: 6.685A pdb=" N ARG A 459 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 470 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A 461 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 468 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1032 through 1038 removed outlier: 5.633A pdb=" N LYS A1034 " --> pdb=" O VAL A1045 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A1045 " --> pdb=" O LYS A1034 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A1036 " --> pdb=" O MET A1043 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR A 976 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A 982 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY A1096 " --> pdb=" O ALA A 982 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 984 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A1094 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 986 " --> pdb=" O GLY A1092 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A1092 " --> pdb=" O MET A 986 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 988 " --> pdb=" O ARG A1090 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG A1090 " --> pdb=" O ALA A 988 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1032 through 1038 removed outlier: 5.633A pdb=" N LYS A1034 " --> pdb=" O VAL A1045 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A1045 " --> pdb=" O LYS A1034 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A1036 " --> pdb=" O MET A1043 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR A 976 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A 982 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY A1096 " --> pdb=" O ALA A 982 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 984 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A1094 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 986 " --> pdb=" O GLY A1092 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A1092 " --> pdb=" O MET A 986 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 988 " --> pdb=" O ARG A1090 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG A1090 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A1091 " --> pdb=" O GLN A1133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 214 removed outlier: 6.910A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU B 289 " --> pdb=" O HIS B 362 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 897 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: 1.80 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1069 1.32 - 1.44: 1723 1.44 - 1.57: 3570 1.57 - 1.69: 5 1.69 - 1.82: 53 Bond restraints: 6420 Sorted by residual: bond pdb=" C8 FOK A1301 " pdb=" O1 FOK A1301 " ideal model delta sigma weight residual 1.419 1.450 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" CB VAL A 376 " pdb=" CG2 VAL A 376 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CG LEU A 953 " pdb=" CD2 LEU A 953 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.66e+00 bond pdb=" C12 FOK A1301 " pdb=" C13 FOK A1301 " ideal model delta sigma weight residual 1.550 1.525 0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C7 FOK A1301 " pdb=" O4 FOK A1301 " ideal model delta sigma weight residual 1.430 1.455 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 6415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 8462 1.81 - 3.61: 170 3.61 - 5.42: 32 5.42 - 7.23: 11 7.23 - 9.04: 3 Bond angle restraints: 8678 Sorted by residual: angle pdb=" CB MET B 221 " pdb=" CG MET B 221 " pdb=" SD MET B 221 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 127.25 -5.71 1.91e+00 2.74e-01 8.94e+00 angle pdb=" CA MET B 110 " pdb=" CB MET B 110 " pdb=" CG MET B 110 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.26e+00 angle pdb=" CB MET B 110 " pdb=" CG MET B 110 " pdb=" SD MET B 110 " ideal model delta sigma weight residual 112.70 120.72 -8.02 3.00e+00 1.11e-01 7.15e+00 angle pdb=" CA MET A 491 " pdb=" CB MET A 491 " pdb=" CG MET A 491 " ideal model delta sigma weight residual 114.10 118.88 -4.78 2.00e+00 2.50e-01 5.70e+00 ... (remaining 8673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3212 17.98 - 35.96: 522 35.96 - 53.94: 139 53.94 - 71.92: 22 71.92 - 89.90: 20 Dihedral angle restraints: 3915 sinusoidal: 1681 harmonic: 2234 Sorted by residual: dihedral pdb=" CB CYS A 457 " pdb=" SG CYS A 457 " pdb=" SG CYS A 469 " pdb=" CB CYS A 469 " ideal model delta sinusoidal sigma weight residual -86.00 -132.37 46.37 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CA ASN A1003 " pdb=" C ASN A1003 " pdb=" N ASN A1004 " pdb=" CA ASN A1004 " ideal model delta harmonic sigma weight residual 180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA HIS A 552 " pdb=" C HIS A 552 " pdb=" N ILE A 553 " pdb=" CA ILE A 553 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 749 0.051 - 0.102: 162 0.102 - 0.152: 27 0.152 - 0.203: 6 0.203 - 0.254: 2 Chirality restraints: 946 Sorted by residual: chirality pdb=" C8 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" C9 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False 2.90 2.65 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR A 494 " pdb=" CA THR A 494 " pdb=" OG1 THR A 494 " pdb=" CG2 THR A 494 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C13 FOK A1301 " pdb=" C12 FOK A1301 " pdb=" C16 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.37 -2.56 0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 943 not shown) Planarity restraints: 1118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO B 115 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 995 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" CG ASP A 995 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP A 995 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 995 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 239 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C ASN B 239 " -0.019 2.00e-02 2.50e+03 pdb=" O ASN B 239 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP B 240 " 0.006 2.00e-02 2.50e+03 ... (remaining 1115 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 54 2.53 - 3.12: 4954 3.12 - 3.71: 10409 3.71 - 4.31: 13343 4.31 - 4.90: 21784 Nonbonded interactions: 50544 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.934 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 1.960 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.119 2.170 nonbonded pdb=" OG1 THR A1000 " pdb=" OD1 ASN A1003 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR B 204 " pdb=" O2G GSP B 501 " model vdw 2.184 3.040 ... (remaining 50539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 12.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.300 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 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 : 0.003 0.050 6420 Z= 0.232 Angle : 0.665 9.037 8678 Z= 0.333 Chirality : 0.046 0.254 946 Planarity : 0.003 0.033 1118 Dihedral : 19.374 89.899 2464 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.59 % Allowed : 35.19 % Favored : 64.22 % 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: -0.26 (0.31), residues: 751 helix: 0.94 (0.28), residues: 346 sheet: 0.19 (0.59), residues: 87 loop : -1.55 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.008 0.001 HIS A 582 PHE 0.016 0.001 PHE B 178 TYR 0.018 0.001 TYR A 468 ARG 0.008 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 454 GLU cc_start: 0.7148 (tp30) cc_final: 0.6748 (tm-30) REVERT: A 555 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7537 (tttt) REVERT: A 971 ASP cc_start: 0.6310 (m-30) cc_final: 0.5609 (t70) REVERT: B 64 HIS cc_start: 0.7098 (p-80) cc_final: 0.6652 (p90) REVERT: B 375 VAL cc_start: 0.4423 (t) cc_final: 0.4208 (m) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 0.2152 time to fit residues: 31.8377 Evaluate side-chains 89 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6420 Z= 0.228 Angle : 0.619 6.249 8678 Z= 0.325 Chirality : 0.044 0.218 946 Planarity : 0.004 0.060 1118 Dihedral : 6.194 48.186 933 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 4.84 % Allowed : 32.70 % Favored : 62.46 % 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: -0.30 (0.30), residues: 751 helix: 0.99 (0.28), residues: 346 sheet: 0.16 (0.59), residues: 90 loop : -1.70 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 281 HIS 0.011 0.001 HIS B 41 PHE 0.021 0.002 PHE B 340 TYR 0.019 0.001 TYR A 468 ARG 0.003 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 419 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6725 (t80) REVERT: A 448 PHE cc_start: 0.4686 (OUTLIER) cc_final: 0.4197 (t80) REVERT: A 454 GLU cc_start: 0.7255 (tp30) cc_final: 0.6852 (tm-30) REVERT: A 467 TYR cc_start: 0.6905 (t80) cc_final: 0.6679 (t80) REVERT: A 555 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7423 (tttt) REVERT: A 971 ASP cc_start: 0.6571 (m-30) cc_final: 0.5807 (t70) REVERT: A 995 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6788 (t0) REVERT: A 1143 LYS cc_start: 0.5059 (OUTLIER) cc_final: 0.4800 (mmtt) REVERT: B 64 HIS cc_start: 0.7023 (p-80) cc_final: 0.6526 (p90) REVERT: B 181 LYS cc_start: 0.7720 (tppt) cc_final: 0.7402 (tppt) REVERT: B 183 ASP cc_start: 0.8313 (p0) cc_final: 0.8083 (t70) outliers start: 33 outliers final: 14 residues processed: 115 average time/residue: 0.1792 time to fit residues: 27.9120 Evaluate side-chains 99 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 69 optimal weight: 0.4980 chunk 74 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 HIS A 528 GLN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6420 Z= 0.182 Angle : 0.578 8.263 8678 Z= 0.299 Chirality : 0.044 0.212 946 Planarity : 0.004 0.043 1118 Dihedral : 5.112 34.650 931 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 4.11 % Allowed : 32.11 % Favored : 63.78 % 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: -0.06 (0.31), residues: 751 helix: 1.33 (0.28), residues: 339 sheet: 0.36 (0.60), residues: 90 loop : -1.71 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 281 HIS 0.005 0.001 HIS B 387 PHE 0.015 0.001 PHE B 340 TYR 0.016 0.001 TYR A 468 ARG 0.002 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 392 MET cc_start: 0.7115 (mtp) cc_final: 0.6880 (mtm) REVERT: A 418 LEU cc_start: 0.7144 (tp) cc_final: 0.6920 (tt) REVERT: A 419 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6657 (t80) REVERT: A 448 PHE cc_start: 0.4727 (OUTLIER) cc_final: 0.4167 (t80) REVERT: A 454 GLU cc_start: 0.7267 (tp30) cc_final: 0.6919 (tm-30) REVERT: A 467 TYR cc_start: 0.6896 (t80) cc_final: 0.6669 (t80) REVERT: A 486 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6306 (mm-30) REVERT: A 541 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6742 (mmmt) REVERT: A 555 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7343 (tttt) REVERT: A 971 ASP cc_start: 0.6587 (m-30) cc_final: 0.5913 (t0) REVERT: B 56 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6468 (tt) REVERT: B 64 HIS cc_start: 0.6896 (p-80) cc_final: 0.6593 (p-80) outliers start: 28 outliers final: 11 residues processed: 110 average time/residue: 0.1978 time to fit residues: 30.3229 Evaluate side-chains 97 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6420 Z= 0.235 Angle : 0.612 8.394 8678 Z= 0.313 Chirality : 0.045 0.252 946 Planarity : 0.004 0.042 1118 Dihedral : 5.213 30.352 931 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 5.87 % Allowed : 30.21 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.31), residues: 751 helix: 1.25 (0.27), residues: 342 sheet: 0.49 (0.66), residues: 75 loop : -1.56 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 281 HIS 0.005 0.001 HIS B 387 PHE 0.045 0.002 PHE B 142 TYR 0.017 0.001 TYR A 468 ARG 0.004 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 84 time to evaluate : 0.777 Fit side-chains REVERT: A 405 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7586 (t70) REVERT: A 419 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6799 (t80) REVERT: A 448 PHE cc_start: 0.4819 (OUTLIER) cc_final: 0.4267 (t80) REVERT: A 454 GLU cc_start: 0.7393 (tp30) cc_final: 0.7019 (tm-30) REVERT: A 486 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6371 (mm-30) REVERT: A 541 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6832 (mmmt) REVERT: A 555 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7525 (tttt) REVERT: A 971 ASP cc_start: 0.6745 (m-30) cc_final: 0.5992 (t0) REVERT: A 1143 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4811 (mmtt) REVERT: B 56 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6515 (tt) REVERT: B 64 HIS cc_start: 0.7093 (p-80) cc_final: 0.6561 (p90) REVERT: B 255 MET cc_start: 0.6996 (mmp) cc_final: 0.6792 (mmp) outliers start: 40 outliers final: 22 residues processed: 113 average time/residue: 0.2176 time to fit residues: 32.5760 Evaluate side-chains 107 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6420 Z= 0.171 Angle : 0.582 10.178 8678 Z= 0.295 Chirality : 0.044 0.302 946 Planarity : 0.004 0.050 1118 Dihedral : 4.914 30.637 931 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 5.43 % Allowed : 30.94 % Favored : 63.64 % 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: 0.00 (0.31), residues: 751 helix: 1.35 (0.27), residues: 344 sheet: 0.42 (0.62), residues: 85 loop : -1.67 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 281 HIS 0.004 0.001 HIS B 387 PHE 0.015 0.001 PHE A1147 TYR 0.014 0.001 TYR A 467 ARG 0.002 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7570 (t70) REVERT: A 419 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6759 (t80) REVERT: A 448 PHE cc_start: 0.4809 (OUTLIER) cc_final: 0.4425 (t80) REVERT: A 454 GLU cc_start: 0.7530 (tp30) cc_final: 0.6947 (tm-30) REVERT: A 455 HIS cc_start: 0.5428 (OUTLIER) cc_final: 0.4307 (m90) REVERT: A 486 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5860 (mm-30) REVERT: A 555 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7453 (tttt) REVERT: A 971 ASP cc_start: 0.6707 (m-30) cc_final: 0.5951 (t0) REVERT: A 1029 PHE cc_start: 0.5660 (OUTLIER) cc_final: 0.5228 (m-80) REVERT: A 1143 LYS cc_start: 0.5129 (OUTLIER) cc_final: 0.4615 (mmtt) REVERT: B 56 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6505 (tt) REVERT: B 64 HIS cc_start: 0.6941 (p-80) cc_final: 0.6400 (p90) REVERT: B 119 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.3868 (mp) REVERT: B 167 ASN cc_start: 0.7486 (m-40) cc_final: 0.7200 (m110) REVERT: B 181 LYS cc_start: 0.8082 (tppt) cc_final: 0.7551 (tppp) outliers start: 37 outliers final: 17 residues processed: 122 average time/residue: 0.1829 time to fit residues: 29.7686 Evaluate side-chains 105 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6420 Z= 0.208 Angle : 0.608 10.378 8678 Z= 0.305 Chirality : 0.044 0.332 946 Planarity : 0.004 0.043 1118 Dihedral : 5.082 29.795 931 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.79 % Favored : 93.08 % Rotamer: Outliers : 6.01 % Allowed : 29.77 % Favored : 64.22 % 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: 0.02 (0.31), residues: 751 helix: 1.40 (0.27), residues: 339 sheet: 0.41 (0.63), residues: 85 loop : -1.65 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 281 HIS 0.004 0.001 HIS B 387 PHE 0.051 0.002 PHE B 142 TYR 0.021 0.001 TYR A 467 ARG 0.004 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 83 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7633 (t70) REVERT: A 419 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6884 (t80) REVERT: A 448 PHE cc_start: 0.4814 (OUTLIER) cc_final: 0.4473 (t80) REVERT: A 454 GLU cc_start: 0.7563 (tp30) cc_final: 0.6971 (tm-30) REVERT: A 455 HIS cc_start: 0.5485 (OUTLIER) cc_final: 0.4411 (m90) REVERT: A 467 TYR cc_start: 0.6874 (t80) cc_final: 0.6629 (t80) REVERT: A 486 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.5869 (mm-30) REVERT: A 555 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7396 (tttt) REVERT: A 971 ASP cc_start: 0.6717 (m-30) cc_final: 0.5968 (t0) REVERT: A 1029 PHE cc_start: 0.5643 (OUTLIER) cc_final: 0.5295 (m-80) REVERT: A 1151 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.4690 (p90) REVERT: B 56 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6537 (tt) REVERT: B 64 HIS cc_start: 0.7060 (p-80) cc_final: 0.6506 (p90) REVERT: B 119 LEU cc_start: 0.4596 (OUTLIER) cc_final: 0.3848 (mp) REVERT: B 181 LYS cc_start: 0.8185 (tppt) cc_final: 0.7662 (tppp) outliers start: 41 outliers final: 23 residues processed: 114 average time/residue: 0.1901 time to fit residues: 28.4820 Evaluate side-chains 112 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6420 Z= 0.211 Angle : 0.624 11.254 8678 Z= 0.313 Chirality : 0.045 0.345 946 Planarity : 0.004 0.053 1118 Dihedral : 5.126 30.638 931 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 5.72 % Allowed : 30.06 % Favored : 64.22 % 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: -0.03 (0.31), residues: 751 helix: 1.29 (0.28), residues: 346 sheet: 0.50 (0.65), residues: 76 loop : -1.63 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 281 HIS 0.006 0.001 HIS A 582 PHE 0.015 0.001 PHE A 448 TYR 0.019 0.001 TYR A 467 ARG 0.003 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 84 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7567 (t70) REVERT: A 419 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6865 (t80) REVERT: A 448 PHE cc_start: 0.4910 (OUTLIER) cc_final: 0.4565 (t80) REVERT: A 454 GLU cc_start: 0.7582 (tp30) cc_final: 0.6999 (tm-30) REVERT: A 455 HIS cc_start: 0.5495 (OUTLIER) cc_final: 0.4556 (m90) REVERT: A 467 TYR cc_start: 0.6874 (t80) cc_final: 0.6653 (t80) REVERT: A 486 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.5859 (mm-30) REVERT: A 555 LYS cc_start: 0.8042 (ttpt) cc_final: 0.7393 (tttt) REVERT: A 971 ASP cc_start: 0.6745 (m-30) cc_final: 0.5984 (t0) REVERT: A 1029 PHE cc_start: 0.5612 (OUTLIER) cc_final: 0.5255 (m-80) REVERT: A 1143 LYS cc_start: 0.5296 (OUTLIER) cc_final: 0.4644 (mmtt) REVERT: A 1151 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.4690 (p90) REVERT: B 56 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6481 (tt) REVERT: B 64 HIS cc_start: 0.7081 (p-80) cc_final: 0.6482 (p90) REVERT: B 119 LEU cc_start: 0.4547 (OUTLIER) cc_final: 0.3854 (mp) REVERT: B 181 LYS cc_start: 0.8189 (tppt) cc_final: 0.7659 (tptp) outliers start: 39 outliers final: 25 residues processed: 113 average time/residue: 0.1772 time to fit residues: 26.9545 Evaluate side-chains 113 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6420 Z= 0.226 Angle : 0.632 11.281 8678 Z= 0.318 Chirality : 0.045 0.333 946 Planarity : 0.004 0.045 1118 Dihedral : 5.261 30.316 931 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 6.16 % Allowed : 29.91 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.31), residues: 751 helix: 1.22 (0.28), residues: 347 sheet: 0.52 (0.65), residues: 76 loop : -1.62 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 281 HIS 0.009 0.001 HIS A 582 PHE 0.053 0.002 PHE B 142 TYR 0.019 0.001 TYR A 467 ARG 0.002 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 82 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7581 (t70) REVERT: A 419 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6831 (t80) REVERT: A 448 PHE cc_start: 0.4892 (OUTLIER) cc_final: 0.4504 (t80) REVERT: A 454 GLU cc_start: 0.7614 (tp30) cc_final: 0.7068 (tm-30) REVERT: A 455 HIS cc_start: 0.5452 (OUTLIER) cc_final: 0.4636 (m90) REVERT: A 467 TYR cc_start: 0.6881 (t80) cc_final: 0.6679 (t80) REVERT: A 486 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6003 (mm-30) REVERT: A 491 MET cc_start: 0.7721 (tmm) cc_final: 0.7446 (tmm) REVERT: A 555 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7459 (tttt) REVERT: A 971 ASP cc_start: 0.6848 (m-30) cc_final: 0.6075 (t0) REVERT: A 1029 PHE cc_start: 0.5710 (OUTLIER) cc_final: 0.5402 (m-80) REVERT: A 1151 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.4747 (p90) REVERT: B 56 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6504 (tt) REVERT: B 64 HIS cc_start: 0.7141 (p-80) cc_final: 0.6399 (p90) REVERT: B 119 LEU cc_start: 0.4525 (OUTLIER) cc_final: 0.3859 (mp) REVERT: B 181 LYS cc_start: 0.8284 (tppt) cc_final: 0.7855 (tppp) REVERT: B 302 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6147 (tt) outliers start: 42 outliers final: 25 residues processed: 112 average time/residue: 0.1974 time to fit residues: 29.8348 Evaluate side-chains 113 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6420 Z= 0.219 Angle : 0.637 12.199 8678 Z= 0.317 Chirality : 0.045 0.343 946 Planarity : 0.004 0.054 1118 Dihedral : 5.250 30.909 931 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 5.13 % Allowed : 30.79 % Favored : 64.08 % 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: -0.05 (0.31), residues: 751 helix: 1.26 (0.27), residues: 346 sheet: 0.48 (0.64), residues: 76 loop : -1.63 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 281 HIS 0.009 0.001 HIS A 582 PHE 0.015 0.002 PHE B 315 TYR 0.018 0.001 TYR A 467 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 83 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7581 (t70) REVERT: A 419 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6737 (t80) REVERT: A 448 PHE cc_start: 0.4838 (OUTLIER) cc_final: 0.4442 (t80) REVERT: A 454 GLU cc_start: 0.7628 (tp30) cc_final: 0.7101 (tm-30) REVERT: A 455 HIS cc_start: 0.5465 (OUTLIER) cc_final: 0.4634 (m90) REVERT: A 486 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6066 (mm-30) REVERT: A 491 MET cc_start: 0.7711 (tmm) cc_final: 0.7411 (tmm) REVERT: A 555 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7407 (tttt) REVERT: A 971 ASP cc_start: 0.6881 (m-30) cc_final: 0.6090 (t0) REVERT: A 1029 PHE cc_start: 0.5760 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: A 1151 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.4793 (p90) REVERT: B 56 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6488 (tt) REVERT: B 64 HIS cc_start: 0.7113 (p-80) cc_final: 0.6363 (p90) REVERT: B 119 LEU cc_start: 0.4516 (OUTLIER) cc_final: 0.3894 (mp) REVERT: B 181 LYS cc_start: 0.8284 (tppt) cc_final: 0.7841 (tptp) REVERT: B 302 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6121 (tt) outliers start: 35 outliers final: 24 residues processed: 109 average time/residue: 0.1439 time to fit residues: 22.0411 Evaluate side-chains 114 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 80 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 0.0000 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6420 Z= 0.231 Angle : 0.648 12.325 8678 Z= 0.323 Chirality : 0.045 0.343 946 Planarity : 0.004 0.048 1118 Dihedral : 5.370 31.467 931 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 5.43 % Allowed : 31.38 % Favored : 63.20 % 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: -0.06 (0.31), residues: 751 helix: 1.31 (0.28), residues: 343 sheet: 0.37 (0.64), residues: 76 loop : -1.65 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 277 HIS 0.009 0.001 HIS A 582 PHE 0.052 0.002 PHE B 142 TYR 0.022 0.001 TYR A 467 ARG 0.006 0.000 ARG A 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 79 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7588 (t70) REVERT: A 419 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6781 (t80) REVERT: A 454 GLU cc_start: 0.7624 (tp30) cc_final: 0.7114 (tm-30) REVERT: A 455 HIS cc_start: 0.5356 (OUTLIER) cc_final: 0.4674 (m90) REVERT: A 486 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6061 (mm-30) REVERT: A 555 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7411 (tttt) REVERT: A 971 ASP cc_start: 0.6990 (m-30) cc_final: 0.6145 (t0) REVERT: A 1029 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5480 (m-80) REVERT: A 1151 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.4994 (p90) REVERT: B 56 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6478 (tt) REVERT: B 64 HIS cc_start: 0.7117 (p-80) cc_final: 0.6417 (p90) REVERT: B 119 LEU cc_start: 0.4525 (OUTLIER) cc_final: 0.3970 (mp) REVERT: B 181 LYS cc_start: 0.8263 (tppt) cc_final: 0.7791 (tptp) REVERT: B 302 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6118 (tt) outliers start: 37 outliers final: 23 residues processed: 107 average time/residue: 0.2028 time to fit residues: 30.3712 Evaluate side-chains 110 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.194378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.166150 restraints weight = 10155.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.170554 restraints weight = 5365.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.173444 restraints weight = 3470.604| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6420 Z= 0.203 Angle : 0.637 12.239 8678 Z= 0.317 Chirality : 0.045 0.333 946 Planarity : 0.004 0.055 1118 Dihedral : 5.208 32.126 931 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 5.13 % Allowed : 31.67 % Favored : 63.20 % 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: -0.11 (0.31), residues: 751 helix: 1.30 (0.28), residues: 347 sheet: 0.31 (0.60), residues: 86 loop : -1.79 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 277 HIS 0.013 0.001 HIS A 582 PHE 0.029 0.002 PHE A 448 TYR 0.018 0.001 TYR A 468 ARG 0.008 0.000 ARG A 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.91 seconds wall clock time: 33 minutes 41.29 seconds (2021.29 seconds total)