Starting phenix.real_space_refine on Thu Jun 12 20:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt5_26111/06_2025/7tt5_26111.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt5_26111/06_2025/7tt5_26111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tt5_26111/06_2025/7tt5_26111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt5_26111/06_2025/7tt5_26111.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt5_26111/06_2025/7tt5_26111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt5_26111/06_2025/7tt5_26111.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.056 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 S 27 5.16 5 C 4636 2.51 5 N 1237 2.21 5 O 1417 1.98 5 H 6938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14255 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2263 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain breaks: 7 Chain: "A" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 7732 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 21, 'TRANS': 483} Chain breaks: 4 Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2423 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 4, 'TRANS': 148} Chain breaks: 3 Chain: "C" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 456 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Time building chain proxies: 7.31, per 1000 atoms: 0.51 Number of scatterers: 14255 At special positions: 0 Unit cell: (91.2747, 104.161, 143.892, 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) S 27 16.00 O 1417 8.00 N 1237 7.00 C 4636 6.00 H 6938 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS P1299 " - pdb=" SG CYS A 425 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.04 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: 3.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 24.6% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.002A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.576A pdb=" N GLN A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 84 through 89 removed outlier: 3.929A pdb=" N GLN D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.572A pdb=" N ASP D 121 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.407A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 152 Processing helix chain 'D' and resid 160 through 189 removed outlier: 3.738A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.646A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.836A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.530A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 Processing sheet with id=AA1, first strand: chain 'P' and resid 1039 through 1045 removed outlier: 3.574A pdb=" N TYR P1108 " --> pdb=" O GLY P1081 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY P1156 " --> pdb=" O TYR P1118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 1159 through 1162 removed outlier: 6.545A pdb=" N ALA P1165 " --> pdb=" O VAL P1161 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL P1208 " --> pdb=" O LEU P1227 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU P1227 " --> pdb=" O VAL P1208 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL P1210 " --> pdb=" O ALA P1225 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA P1225 " --> pdb=" O VAL P1210 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS P1212 " --> pdb=" O ALA P1223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA P1223 " --> pdb=" O LYS P1212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU P1276 " --> pdb=" O LEU P1264 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE P1274 " --> pdb=" O ALA P1266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 425 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 524 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 530 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 636 " --> pdb=" O MET A 711 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 711 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 803 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.504A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.605A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.605A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1032 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: 5.09 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6938 1.04 - 1.23: 397 1.23 - 1.43: 2953 1.43 - 1.63: 4082 1.63 - 1.83: 50 Bond restraints: 14420 Sorted by residual: bond pdb=" CA PHE A 395 " pdb=" CB PHE A 395 " ideal model delta sigma weight residual 1.536 1.504 0.032 2.53e-02 1.56e+03 1.63e+00 bond pdb=" CA ALA D 193 " pdb=" C ALA D 193 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.35e-02 5.49e+03 1.23e+00 bond pdb=" CG LEU A 365 " pdb=" CD2 LEU A 365 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CB PHE A 395 " pdb=" CG PHE A 395 " ideal model delta sigma weight residual 1.502 1.478 0.024 2.30e-02 1.89e+03 1.06e+00 bond pdb=" CG PRO A 587 " pdb=" CD PRO A 587 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.57e-01 ... (remaining 14415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 24480 1.25 - 2.51: 1209 2.51 - 3.76: 110 3.76 - 5.02: 15 5.02 - 6.27: 3 Bond angle restraints: 25817 Sorted by residual: angle pdb=" N ASP P1270 " pdb=" CA ASP P1270 " pdb=" C ASP P1270 " ideal model delta sigma weight residual 110.80 117.07 -6.27 2.13e+00 2.20e-01 8.67e+00 angle pdb=" N GLN D 224 " pdb=" CA GLN D 224 " pdb=" C GLN D 224 " ideal model delta sigma weight residual 113.18 109.62 3.56 1.21e+00 6.83e-01 8.65e+00 angle pdb=" N TYR P1286 " pdb=" CA TYR P1286 " pdb=" C TYR P1286 " ideal model delta sigma weight residual 109.50 105.09 4.41 1.58e+00 4.01e-01 7.79e+00 angle pdb=" N ASP A 569 " pdb=" CA ASP A 569 " pdb=" C ASP A 569 " ideal model delta sigma weight residual 108.41 112.93 -4.52 1.63e+00 3.76e-01 7.70e+00 angle pdb=" N ASP A 410 " pdb=" CA ASP A 410 " pdb=" C ASP A 410 " ideal model delta sigma weight residual 111.87 115.72 -3.85 1.41e+00 5.03e-01 7.45e+00 ... (remaining 25812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6499 17.55 - 35.11: 196 35.11 - 52.66: 129 52.66 - 70.21: 37 70.21 - 87.77: 8 Dihedral angle restraints: 6869 sinusoidal: 3615 harmonic: 3254 Sorted by residual: dihedral pdb=" CA CYS P1299 " pdb=" CB CYS P1299 " pdb=" SG CYS P1299 " pdb=" SG CYS A 425 " ideal model delta sinusoidal sigma weight residual -73.00 -20.09 -52.91 1 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CB GLU E 84 " pdb=" CG GLU E 84 " pdb=" CD GLU E 84 " pdb=" OE1 GLU E 84 " ideal model delta sinusoidal sigma weight residual 0.00 -79.09 79.09 1 3.00e+01 1.11e-03 8.65e+00 dihedral pdb=" CB GLU A 272 " pdb=" CG GLU A 272 " pdb=" CD GLU A 272 " pdb=" OE1 GLU A 272 " ideal model delta sinusoidal sigma weight residual 0.00 -76.55 76.55 1 3.00e+01 1.11e-03 8.19e+00 ... (remaining 6866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 599 0.027 - 0.053: 268 0.053 - 0.080: 93 0.080 - 0.107: 71 0.107 - 0.133: 34 Chirality restraints: 1065 Sorted by residual: chirality pdb=" CA PRO A 409 " pdb=" N PRO A 409 " pdb=" C PRO A 409 " pdb=" CB PRO A 409 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL A 513 " pdb=" N VAL A 513 " pdb=" C VAL A 513 " pdb=" CB VAL A 513 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL A 744 " pdb=" N VAL A 744 " pdb=" C VAL A 744 " pdb=" CB VAL A 744 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1062 not shown) Planarity restraints: 2199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 586 " -0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO A 587 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU P1168 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO P1169 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO P1169 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO P1169 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 136 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO D 137 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 137 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 137 " 0.032 5.00e-02 4.00e+02 ... (remaining 2196 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 388 2.14 - 2.76: 26265 2.76 - 3.37: 36226 3.37 - 3.99: 46968 3.99 - 4.60: 73322 Nonbonded interactions: 183169 Sorted by model distance: nonbonded pdb="HD22 ASN P1271 " pdb=" O CYS P1299 " model vdw 1.528 2.450 nonbonded pdb=" OD1 ASP D 136 " pdb=" H GLN D 138 " model vdw 1.571 2.450 nonbonded pdb=" H ILE A 352 " pdb=" OE2 GLU A 373 " model vdw 1.601 2.450 nonbonded pdb=" OD2 ASP A 703 " pdb=" HZ1 LYS A 798 " model vdw 1.611 2.450 nonbonded pdb=" OD1 ASP D 172 " pdb=" HG1 THR D 208 " model vdw 1.614 2.450 ... (remaining 183164 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: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.260 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.100 Find NCS groups from input model: 0.100 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.004 0.035 7484 Z= 0.184 Angle : 0.695 6.271 10135 Z= 0.429 Chirality : 0.043 0.133 1065 Planarity : 0.005 0.088 1325 Dihedral : 10.021 87.766 2667 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 890 helix: -0.22 (0.33), residues: 193 sheet: 1.43 (0.26), residues: 347 loop : 1.06 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 546 HIS 0.002 0.001 HIS D 139 PHE 0.035 0.002 PHE A 395 TYR 0.024 0.002 TYR A 348 ARG 0.017 0.002 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.24200 ( 367) hydrogen bonds : angle 8.96895 ( 1032) SS BOND : bond 0.00860 ( 2) SS BOND : angle 1.90727 ( 4) covalent geometry : bond 0.00376 ( 7482) covalent geometry : angle 0.69408 (10131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1265 ASN cc_start: 0.9638 (m-40) cc_final: 0.9437 (p0) REVERT: P 1296 PHE cc_start: 0.9284 (t80) cc_final: 0.8766 (t80) REVERT: A 306 ASP cc_start: 0.9382 (m-30) cc_final: 0.8469 (m-30) REVERT: A 372 MET cc_start: 0.8203 (mmp) cc_final: 0.7708 (mmm) REVERT: A 386 LYS cc_start: 0.9361 (tttt) cc_final: 0.9114 (ttpt) REVERT: A 388 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8438 (tpp-160) REVERT: A 440 PHE cc_start: 0.8256 (m-80) cc_final: 0.7859 (m-10) REVERT: A 474 THR cc_start: 0.9117 (m) cc_final: 0.8865 (p) REVERT: A 491 TYR cc_start: 0.8490 (t80) cc_final: 0.8157 (t80) REVERT: A 535 SER cc_start: 0.7688 (t) cc_final: 0.7405 (t) REVERT: A 582 ASP cc_start: 0.8688 (p0) cc_final: 0.8207 (t70) REVERT: A 637 TYR cc_start: 0.8225 (t80) cc_final: 0.7884 (t80) REVERT: A 711 MET cc_start: 0.8728 (ppp) cc_final: 0.8099 (ppp) REVERT: A 741 MET cc_start: 0.8245 (pmm) cc_final: 0.7763 (pmm) REVERT: A 765 ASN cc_start: 0.9266 (m-40) cc_final: 0.8941 (m-40) REVERT: E 27 VAL cc_start: 0.9545 (t) cc_final: 0.9265 (m) REVERT: E 42 ASP cc_start: 0.9189 (m-30) cc_final: 0.8755 (m-30) REVERT: E 80 GLN cc_start: 0.8881 (tt0) cc_final: 0.8570 (tp-100) REVERT: E 84 GLU cc_start: 0.8532 (tp30) cc_final: 0.8256 (mm-30) REVERT: E 90 THR cc_start: 0.8901 (m) cc_final: 0.8375 (m) REVERT: D 84 ASP cc_start: 0.8424 (m-30) cc_final: 0.7101 (m-30) REVERT: D 131 ASP cc_start: 0.7846 (t0) cc_final: 0.7622 (t0) REVERT: D 136 ASP cc_start: 0.9341 (t0) cc_final: 0.8239 (t0) REVERT: D 213 ASP cc_start: 0.8557 (m-30) cc_final: 0.8156 (t70) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.4741 time to fit residues: 184.1533 Evaluate side-chains 209 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN D 82 ASN D 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.143519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095504 restraints weight = 40161.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099826 restraints weight = 19163.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102614 restraints weight = 12408.293| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 7484 Z= 0.145 Angle : 0.597 15.440 10135 Z= 0.336 Chirality : 0.044 0.187 1065 Planarity : 0.005 0.063 1325 Dihedral : 4.433 41.576 1018 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.28), residues: 890 helix: 1.67 (0.38), residues: 193 sheet: 1.04 (0.26), residues: 356 loop : 0.88 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.005 0.001 HIS A 533 PHE 0.015 0.002 PHE A 426 TYR 0.027 0.001 TYR A 550 ARG 0.007 0.001 ARG P1269 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 367) hydrogen bonds : angle 6.64871 ( 1032) SS BOND : bond 0.01698 ( 2) SS BOND : angle 4.99660 ( 4) covalent geometry : bond 0.00323 ( 7482) covalent geometry : angle 0.58832 (10131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1271 ASN cc_start: 0.8355 (p0) cc_final: 0.8130 (p0) REVERT: A 307 ASP cc_start: 0.9143 (m-30) cc_final: 0.8933 (m-30) REVERT: A 350 ARG cc_start: 0.8639 (ttt90) cc_final: 0.8298 (ttt-90) REVERT: A 386 LYS cc_start: 0.9303 (tttt) cc_final: 0.8976 (ttpt) REVERT: A 408 SER cc_start: 0.8769 (t) cc_final: 0.8499 (t) REVERT: A 474 THR cc_start: 0.9090 (m) cc_final: 0.8792 (p) REVERT: A 535 SER cc_start: 0.8408 (t) cc_final: 0.8108 (p) REVERT: A 582 ASP cc_start: 0.9051 (p0) cc_final: 0.8230 (t0) REVERT: A 635 TRP cc_start: 0.8397 (m100) cc_final: 0.8045 (m-10) REVERT: A 637 TYR cc_start: 0.8082 (t80) cc_final: 0.7771 (t80) REVERT: A 711 MET cc_start: 0.8705 (ppp) cc_final: 0.8070 (ppp) REVERT: A 741 MET cc_start: 0.7988 (pmm) cc_final: 0.7546 (pmm) REVERT: A 765 ASN cc_start: 0.9238 (m-40) cc_final: 0.9018 (m-40) REVERT: E 46 ILE cc_start: 0.9026 (mm) cc_final: 0.8819 (mp) REVERT: E 80 GLN cc_start: 0.8856 (tt0) cc_final: 0.8617 (tp-100) REVERT: E 105 ASP cc_start: 0.7431 (m-30) cc_final: 0.7007 (m-30) REVERT: D 84 ASP cc_start: 0.8177 (m-30) cc_final: 0.7969 (t0) REVERT: D 87 LEU cc_start: 0.9482 (mt) cc_final: 0.9115 (mt) REVERT: D 131 ASP cc_start: 0.7997 (t0) cc_final: 0.7786 (t0) REVERT: D 204 ASP cc_start: 0.8324 (t70) cc_final: 0.8003 (t0) REVERT: D 213 ASP cc_start: 0.8497 (m-30) cc_final: 0.8031 (t70) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.4165 time to fit residues: 129.0485 Evaluate side-chains 206 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 9.9990 chunk 68 optimal weight: 0.0670 chunk 76 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095799 restraints weight = 41309.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100419 restraints weight = 19287.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103350 restraints weight = 12345.941| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 7484 Z= 0.115 Angle : 0.513 10.251 10135 Z= 0.287 Chirality : 0.043 0.162 1065 Planarity : 0.004 0.053 1325 Dihedral : 4.328 49.249 1018 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.28), residues: 890 helix: 1.83 (0.38), residues: 199 sheet: 0.68 (0.26), residues: 346 loop : 0.93 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 576 HIS 0.004 0.001 HIS A 533 PHE 0.012 0.001 PHE A 718 TYR 0.017 0.001 TYR A 550 ARG 0.007 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 367) hydrogen bonds : angle 5.95280 ( 1032) SS BOND : bond 0.01072 ( 2) SS BOND : angle 2.87321 ( 4) covalent geometry : bond 0.00249 ( 7482) covalent geometry : angle 0.51009 (10131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1271 ASN cc_start: 0.8490 (p0) cc_final: 0.8229 (p0) REVERT: A 307 ASP cc_start: 0.9108 (m-30) cc_final: 0.8903 (m-30) REVERT: A 386 LYS cc_start: 0.9327 (tttt) cc_final: 0.9001 (ttpt) REVERT: A 474 THR cc_start: 0.9106 (m) cc_final: 0.8818 (p) REVERT: A 582 ASP cc_start: 0.9140 (p0) cc_final: 0.8164 (t0) REVERT: A 609 TYR cc_start: 0.8474 (p90) cc_final: 0.8243 (p90) REVERT: A 614 ASP cc_start: 0.8713 (t70) cc_final: 0.8338 (t0) REVERT: A 635 TRP cc_start: 0.8425 (m100) cc_final: 0.8067 (m-10) REVERT: A 711 MET cc_start: 0.8749 (ppp) cc_final: 0.8098 (ppp) REVERT: A 741 MET cc_start: 0.7991 (pmm) cc_final: 0.7555 (pmm) REVERT: A 765 ASN cc_start: 0.9235 (m-40) cc_final: 0.9003 (m-40) REVERT: E 46 ILE cc_start: 0.9050 (mm) cc_final: 0.8828 (mp) REVERT: E 83 HIS cc_start: 0.8371 (p-80) cc_final: 0.7759 (p90) REVERT: E 105 ASP cc_start: 0.7372 (m-30) cc_final: 0.6989 (m-30) REVERT: D 87 LEU cc_start: 0.9484 (mt) cc_final: 0.9172 (mt) REVERT: D 199 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 49 GLU cc_start: 0.8414 (pm20) cc_final: 0.8201 (pm20) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.4503 time to fit residues: 132.3313 Evaluate side-chains 200 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 3 optimal weight: 40.0000 chunk 0 optimal weight: 90.0000 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.091456 restraints weight = 41199.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095544 restraints weight = 20033.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098116 restraints weight = 13214.146| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7484 Z= 0.175 Angle : 0.525 7.201 10135 Z= 0.295 Chirality : 0.042 0.152 1065 Planarity : 0.004 0.047 1325 Dihedral : 4.484 51.317 1018 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.28), residues: 890 helix: 1.47 (0.37), residues: 199 sheet: 0.36 (0.26), residues: 351 loop : 0.69 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 48 HIS 0.006 0.001 HIS E 83 PHE 0.014 0.001 PHE A 395 TYR 0.028 0.001 TYR A 550 ARG 0.007 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 367) hydrogen bonds : angle 5.72264 ( 1032) SS BOND : bond 0.00775 ( 2) SS BOND : angle 2.23374 ( 4) covalent geometry : bond 0.00379 ( 7482) covalent geometry : angle 0.52330 (10131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1112 MET cc_start: 0.9043 (ppp) cc_final: 0.8602 (pmm) REVERT: P 1260 MET cc_start: 0.8874 (mtm) cc_final: 0.8609 (mpp) REVERT: P 1270 ASP cc_start: 0.9098 (p0) cc_final: 0.8555 (p0) REVERT: P 1271 ASN cc_start: 0.8507 (p0) cc_final: 0.8192 (p0) REVERT: A 386 LYS cc_start: 0.9371 (tttt) cc_final: 0.9059 (ttpt) REVERT: A 445 GLN cc_start: 0.8911 (pt0) cc_final: 0.8212 (pp30) REVERT: A 474 THR cc_start: 0.9140 (m) cc_final: 0.8846 (p) REVERT: A 550 TYR cc_start: 0.8732 (m-80) cc_final: 0.8510 (m-80) REVERT: A 614 ASP cc_start: 0.8798 (t70) cc_final: 0.8507 (t0) REVERT: A 635 TRP cc_start: 0.8492 (m100) cc_final: 0.8184 (m-10) REVERT: A 637 TYR cc_start: 0.8044 (t80) cc_final: 0.7644 (t80) REVERT: A 711 MET cc_start: 0.8864 (ppp) cc_final: 0.8196 (ppp) REVERT: A 765 ASN cc_start: 0.9241 (m-40) cc_final: 0.9037 (m-40) REVERT: E 46 ILE cc_start: 0.9137 (mm) cc_final: 0.8855 (mp) REVERT: E 65 SER cc_start: 0.9161 (p) cc_final: 0.8887 (t) REVERT: E 105 ASP cc_start: 0.7360 (m-30) cc_final: 0.7011 (m-30) REVERT: D 84 ASP cc_start: 0.8027 (t0) cc_final: 0.7713 (t0) REVERT: D 136 ASP cc_start: 0.8898 (t0) cc_final: 0.8542 (t0) REVERT: D 199 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8015 (tm-30) REVERT: D 213 ASP cc_start: 0.8503 (m-30) cc_final: 0.8095 (t70) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.4615 time to fit residues: 129.7854 Evaluate side-chains 186 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.089994 restraints weight = 41886.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.094070 restraints weight = 20235.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096628 restraints weight = 13374.617| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 7484 Z= 0.177 Angle : 0.600 23.050 10135 Z= 0.325 Chirality : 0.044 0.436 1065 Planarity : 0.004 0.054 1325 Dihedral : 4.673 51.100 1018 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.26 % Allowed : 0.53 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.65 (0.28), residues: 890 helix: 1.37 (0.37), residues: 199 sheet: 0.16 (0.26), residues: 344 loop : 0.38 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 48 HIS 0.007 0.001 HIS E 83 PHE 0.019 0.002 PHE A 648 TYR 0.017 0.001 TYR A 550 ARG 0.008 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 367) hydrogen bonds : angle 5.59076 ( 1032) SS BOND : bond 0.02894 ( 2) SS BOND : angle 5.84305 ( 4) covalent geometry : bond 0.00384 ( 7482) covalent geometry : angle 0.58912 (10131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1112 MET cc_start: 0.9082 (ppp) cc_final: 0.8722 (pmm) REVERT: P 1217 LYS cc_start: 0.9280 (tptp) cc_final: 0.8831 (mmtp) REVERT: A 307 ASP cc_start: 0.9056 (m-30) cc_final: 0.8849 (m-30) REVERT: A 371 GLN cc_start: 0.8394 (tp-100) cc_final: 0.8152 (tp-100) REVERT: A 386 LYS cc_start: 0.9366 (tttt) cc_final: 0.9074 (ttpt) REVERT: A 445 GLN cc_start: 0.8786 (pt0) cc_final: 0.8080 (pp30) REVERT: A 474 THR cc_start: 0.9173 (m) cc_final: 0.8921 (p) REVERT: A 535 SER cc_start: 0.8260 (t) cc_final: 0.7966 (m) REVERT: A 614 ASP cc_start: 0.8812 (t70) cc_final: 0.8572 (t0) REVERT: A 637 TYR cc_start: 0.8108 (t80) cc_final: 0.7683 (t80) REVERT: A 711 MET cc_start: 0.8920 (ppp) cc_final: 0.8257 (ppp) REVERT: E 46 ILE cc_start: 0.9128 (mm) cc_final: 0.8798 (mp) REVERT: E 65 SER cc_start: 0.9030 (p) cc_final: 0.8814 (t) REVERT: E 105 ASP cc_start: 0.7282 (m-30) cc_final: 0.6975 (m-30) REVERT: D 84 ASP cc_start: 0.7969 (t0) cc_final: 0.7687 (t0) REVERT: D 136 ASP cc_start: 0.8968 (t0) cc_final: 0.8609 (t0) REVERT: D 199 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8025 (tm-30) REVERT: D 213 ASP cc_start: 0.8462 (m-30) cc_final: 0.8096 (t70) outliers start: 2 outliers final: 1 residues processed: 210 average time/residue: 0.4531 time to fit residues: 123.8624 Evaluate side-chains 186 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 5 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 chunk 83 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087870 restraints weight = 42861.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.092354 restraints weight = 19615.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095107 restraints weight = 12544.517| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7484 Z= 0.187 Angle : 0.551 11.268 10135 Z= 0.307 Chirality : 0.042 0.247 1065 Planarity : 0.004 0.057 1325 Dihedral : 4.929 55.935 1018 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.38 (0.27), residues: 890 helix: 1.17 (0.36), residues: 199 sheet: 0.00 (0.26), residues: 344 loop : 0.18 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 576 HIS 0.005 0.001 HIS E 83 PHE 0.024 0.002 PHE E 74 TYR 0.021 0.001 TYR D 205 ARG 0.010 0.001 ARG P1269 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 367) hydrogen bonds : angle 5.56773 ( 1032) SS BOND : bond 0.00435 ( 2) SS BOND : angle 4.66335 ( 4) covalent geometry : bond 0.00402 ( 7482) covalent geometry : angle 0.54303 (10131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1112 MET cc_start: 0.9208 (ppp) cc_final: 0.8859 (pmm) REVERT: P 1217 LYS cc_start: 0.9316 (tptp) cc_final: 0.8843 (mmtp) REVERT: A 307 ASP cc_start: 0.9089 (m-30) cc_final: 0.8872 (m-30) REVERT: A 386 LYS cc_start: 0.9386 (tttt) cc_final: 0.9103 (ttpt) REVERT: A 550 TYR cc_start: 0.8787 (m-80) cc_final: 0.8535 (m-80) REVERT: A 711 MET cc_start: 0.8956 (ppp) cc_final: 0.8580 (ppp) REVERT: E 46 ILE cc_start: 0.9157 (mm) cc_final: 0.8756 (mp) REVERT: E 65 SER cc_start: 0.8988 (p) cc_final: 0.8722 (t) REVERT: E 88 GLN cc_start: 0.7758 (pp30) cc_final: 0.7538 (pp30) REVERT: E 105 ASP cc_start: 0.7254 (m-30) cc_final: 0.6992 (m-30) REVERT: D 84 ASP cc_start: 0.8004 (t0) cc_final: 0.7644 (t0) REVERT: D 199 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8037 (tm-30) REVERT: D 207 ASP cc_start: 0.8381 (p0) cc_final: 0.7808 (p0) REVERT: D 213 ASP cc_start: 0.8478 (m-30) cc_final: 0.8112 (t70) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.4444 time to fit residues: 117.0007 Evaluate side-chains 174 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 50.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094516 restraints weight = 41555.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098773 restraints weight = 20129.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101467 restraints weight = 13233.573| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7484 Z= 0.113 Angle : 0.511 9.772 10135 Z= 0.279 Chirality : 0.042 0.233 1065 Planarity : 0.004 0.064 1325 Dihedral : 4.683 48.120 1018 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.13 % Allowed : 0.53 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.54 (0.28), residues: 890 helix: 1.47 (0.37), residues: 199 sheet: 0.07 (0.26), residues: 335 loop : 0.19 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 191 HIS 0.006 0.001 HIS E 83 PHE 0.030 0.001 PHE A 738 TYR 0.013 0.001 TYR A 550 ARG 0.011 0.000 ARG P1269 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 367) hydrogen bonds : angle 5.24134 ( 1032) SS BOND : bond 0.00439 ( 2) SS BOND : angle 3.86567 ( 4) covalent geometry : bond 0.00243 ( 7482) covalent geometry : angle 0.50527 (10131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1112 MET cc_start: 0.8995 (ppp) cc_final: 0.8739 (pmm) REVERT: P 1159 TYR cc_start: 0.8712 (t80) cc_final: 0.8232 (t80) REVERT: P 1217 LYS cc_start: 0.9249 (tptp) cc_final: 0.8826 (mmtp) REVERT: A 386 LYS cc_start: 0.9366 (tttt) cc_final: 0.9099 (ttpt) REVERT: A 445 GLN cc_start: 0.8625 (pt0) cc_final: 0.8058 (pp30) REVERT: A 474 THR cc_start: 0.9156 (m) cc_final: 0.8921 (p) REVERT: A 635 TRP cc_start: 0.8355 (m-10) cc_final: 0.7973 (m-10) REVERT: A 637 TYR cc_start: 0.8073 (t80) cc_final: 0.7763 (t80) REVERT: A 711 MET cc_start: 0.8993 (ppp) cc_final: 0.8334 (ppp) REVERT: A 765 ASN cc_start: 0.9100 (m110) cc_final: 0.8726 (m-40) REVERT: E 46 ILE cc_start: 0.9085 (mm) cc_final: 0.8724 (mp) REVERT: D 84 ASP cc_start: 0.8102 (t0) cc_final: 0.7703 (t0) REVERT: D 149 LYS cc_start: 0.8832 (mmpt) cc_final: 0.8396 (tppt) REVERT: D 207 ASP cc_start: 0.8283 (p0) cc_final: 0.7673 (p0) REVERT: D 213 ASP cc_start: 0.8324 (m-30) cc_final: 0.8038 (t70) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.4758 time to fit residues: 130.6940 Evaluate side-chains 179 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 0.0170 chunk 83 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.090553 restraints weight = 41880.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095190 restraints weight = 18829.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098219 restraints weight = 12062.050| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7484 Z= 0.099 Angle : 0.486 7.136 10135 Z= 0.263 Chirality : 0.042 0.204 1065 Planarity : 0.003 0.043 1325 Dihedral : 4.501 42.288 1018 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.62 (0.28), residues: 890 helix: 1.65 (0.37), residues: 199 sheet: 0.03 (0.26), residues: 343 loop : 0.29 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 191 HIS 0.006 0.001 HIS E 83 PHE 0.018 0.001 PHE A 648 TYR 0.013 0.001 TYR A 550 ARG 0.003 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 367) hydrogen bonds : angle 5.02879 ( 1032) SS BOND : bond 0.00191 ( 2) SS BOND : angle 3.10592 ( 4) covalent geometry : bond 0.00214 ( 7482) covalent geometry : angle 0.48259 (10131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1112 MET cc_start: 0.9106 (ppp) cc_final: 0.8814 (pmm) REVERT: P 1159 TYR cc_start: 0.8862 (t80) cc_final: 0.8507 (t80) REVERT: A 307 ASP cc_start: 0.9064 (m-30) cc_final: 0.8864 (m-30) REVERT: A 352 ILE cc_start: 0.9207 (mt) cc_final: 0.8728 (tt) REVERT: A 386 LYS cc_start: 0.9381 (tttt) cc_final: 0.9038 (ttpt) REVERT: A 445 GLN cc_start: 0.8723 (pt0) cc_final: 0.8050 (pp30) REVERT: A 474 THR cc_start: 0.9156 (m) cc_final: 0.8922 (p) REVERT: A 582 ASP cc_start: 0.9035 (p0) cc_final: 0.8348 (t0) REVERT: A 635 TRP cc_start: 0.8324 (m-10) cc_final: 0.7900 (m-10) REVERT: A 711 MET cc_start: 0.8962 (ppp) cc_final: 0.8329 (ppp) REVERT: A 765 ASN cc_start: 0.9141 (m110) cc_final: 0.8749 (m-40) REVERT: E 46 ILE cc_start: 0.9170 (mm) cc_final: 0.8813 (mp) REVERT: E 105 ASP cc_start: 0.7470 (m-30) cc_final: 0.6511 (m-30) REVERT: D 53 THR cc_start: 0.9034 (m) cc_final: 0.8828 (p) REVERT: D 84 ASP cc_start: 0.8002 (t0) cc_final: 0.7578 (t0) REVERT: D 207 ASP cc_start: 0.8319 (p0) cc_final: 0.7779 (p0) REVERT: D 213 ASP cc_start: 0.8535 (m-30) cc_final: 0.8152 (t70) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.4666 time to fit residues: 124.6790 Evaluate side-chains 182 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 50.0000 chunk 51 optimal weight: 0.0570 chunk 52 optimal weight: 6.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.089630 restraints weight = 42279.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.094347 restraints weight = 19134.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097314 restraints weight = 12198.242| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7484 Z= 0.113 Angle : 0.496 7.746 10135 Z= 0.266 Chirality : 0.042 0.220 1065 Planarity : 0.003 0.044 1325 Dihedral : 4.514 45.578 1018 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.56 (0.28), residues: 890 helix: 1.61 (0.37), residues: 199 sheet: 0.03 (0.26), residues: 346 loop : 0.19 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 191 HIS 0.006 0.001 HIS E 83 PHE 0.017 0.001 PHE P1300 TYR 0.012 0.001 TYR D 184 ARG 0.004 0.000 ARG P1224 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 367) hydrogen bonds : angle 4.98112 ( 1032) SS BOND : bond 0.00334 ( 2) SS BOND : angle 2.99661 ( 4) covalent geometry : bond 0.00248 ( 7482) covalent geometry : angle 0.49220 (10131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1112 MET cc_start: 0.9081 (ppp) cc_final: 0.8803 (pmm) REVERT: P 1159 TYR cc_start: 0.8812 (t80) cc_final: 0.8323 (t80) REVERT: A 307 ASP cc_start: 0.9045 (m-30) cc_final: 0.8829 (m-30) REVERT: A 352 ILE cc_start: 0.9208 (mt) cc_final: 0.8741 (tt) REVERT: A 386 LYS cc_start: 0.9395 (tttt) cc_final: 0.9091 (ttpt) REVERT: A 445 GLN cc_start: 0.8744 (pt0) cc_final: 0.8102 (pp30) REVERT: A 635 TRP cc_start: 0.8367 (m-10) cc_final: 0.7982 (m-10) REVERT: A 703 ASP cc_start: 0.8557 (p0) cc_final: 0.8201 (p0) REVERT: A 711 MET cc_start: 0.8967 (ppp) cc_final: 0.8347 (ppp) REVERT: A 765 ASN cc_start: 0.9162 (m110) cc_final: 0.8785 (m-40) REVERT: E 46 ILE cc_start: 0.9158 (mm) cc_final: 0.8778 (mp) REVERT: E 88 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7441 (pp30) REVERT: E 105 ASP cc_start: 0.7338 (m-30) cc_final: 0.6472 (m-30) REVERT: D 53 THR cc_start: 0.9027 (m) cc_final: 0.8735 (p) REVERT: D 84 ASP cc_start: 0.8063 (t0) cc_final: 0.7647 (t0) REVERT: D 136 ASP cc_start: 0.8876 (t0) cc_final: 0.8655 (t0) REVERT: D 149 LYS cc_start: 0.8863 (mmpt) cc_final: 0.8489 (tppt) REVERT: D 207 ASP cc_start: 0.8312 (p0) cc_final: 0.7824 (p0) REVERT: D 213 ASP cc_start: 0.8478 (m-30) cc_final: 0.8101 (t70) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.4558 time to fit residues: 124.7730 Evaluate side-chains 182 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 50.0000 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 83 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.089206 restraints weight = 42853.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093932 restraints weight = 19373.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.096935 restraints weight = 12420.527| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7484 Z= 0.114 Angle : 0.499 7.222 10135 Z= 0.269 Chirality : 0.042 0.210 1065 Planarity : 0.004 0.076 1325 Dihedral : 4.461 43.622 1018 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.54 (0.28), residues: 890 helix: 1.58 (0.37), residues: 199 sheet: 0.03 (0.26), residues: 346 loop : 0.17 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 546 HIS 0.007 0.001 HIS E 83 PHE 0.019 0.001 PHE P1300 TYR 0.025 0.001 TYR A 550 ARG 0.014 0.001 ARG P1269 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 367) hydrogen bonds : angle 4.93304 ( 1032) SS BOND : bond 0.00195 ( 2) SS BOND : angle 2.65985 ( 4) covalent geometry : bond 0.00251 ( 7482) covalent geometry : angle 0.49645 (10131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1112 MET cc_start: 0.9142 (ppp) cc_final: 0.8885 (pmm) REVERT: P 1159 TYR cc_start: 0.8854 (t80) cc_final: 0.8549 (t80) REVERT: P 1274 PHE cc_start: 0.9131 (t80) cc_final: 0.8872 (t80) REVERT: A 307 ASP cc_start: 0.9065 (m-30) cc_final: 0.8856 (m-30) REVERT: A 352 ILE cc_start: 0.9199 (mt) cc_final: 0.8741 (tt) REVERT: A 386 LYS cc_start: 0.9390 (tttt) cc_final: 0.9097 (ttpt) REVERT: A 445 GLN cc_start: 0.8762 (pt0) cc_final: 0.8127 (pp30) REVERT: A 550 TYR cc_start: 0.8710 (m-80) cc_final: 0.8412 (m-80) REVERT: A 635 TRP cc_start: 0.8381 (m-10) cc_final: 0.8007 (m-10) REVERT: A 703 ASP cc_start: 0.8431 (p0) cc_final: 0.8040 (p0) REVERT: A 711 MET cc_start: 0.8971 (ppp) cc_final: 0.8350 (ppp) REVERT: A 765 ASN cc_start: 0.9186 (m110) cc_final: 0.8807 (m-40) REVERT: E 46 ILE cc_start: 0.9136 (mm) cc_final: 0.8822 (mp) REVERT: E 105 ASP cc_start: 0.7217 (m-30) cc_final: 0.6352 (m-30) REVERT: D 53 THR cc_start: 0.9063 (m) cc_final: 0.8765 (p) REVERT: D 84 ASP cc_start: 0.8060 (t0) cc_final: 0.7640 (t0) REVERT: D 136 ASP cc_start: 0.8889 (t0) cc_final: 0.8651 (t0) REVERT: D 149 LYS cc_start: 0.8846 (mmpt) cc_final: 0.8455 (tppt) REVERT: D 207 ASP cc_start: 0.8329 (p0) cc_final: 0.7842 (p0) REVERT: D 213 ASP cc_start: 0.8499 (m-30) cc_final: 0.8120 (t70) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.4346 time to fit residues: 113.9909 Evaluate side-chains 181 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 100.0000 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.139945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.087665 restraints weight = 43518.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.092329 restraints weight = 19671.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095262 restraints weight = 12691.886| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7484 Z= 0.145 Angle : 0.509 7.320 10135 Z= 0.278 Chirality : 0.042 0.212 1065 Planarity : 0.004 0.047 1325 Dihedral : 4.480 42.907 1018 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.42 (0.28), residues: 890 helix: 1.52 (0.37), residues: 199 sheet: -0.06 (0.26), residues: 346 loop : 0.10 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P1166 HIS 0.006 0.001 HIS E 83 PHE 0.020 0.001 PHE P1300 TYR 0.019 0.001 TYR A 550 ARG 0.019 0.001 ARG P1158 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 367) hydrogen bonds : angle 5.00457 ( 1032) SS BOND : bond 0.00193 ( 2) SS BOND : angle 2.77568 ( 4) covalent geometry : bond 0.00316 ( 7482) covalent geometry : angle 0.50611 (10131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5461.34 seconds wall clock time: 93 minutes 46.27 seconds (5626.27 seconds total)