Starting phenix.real_space_refine on Thu Sep 18 05:16:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt5_26111/09_2025/7tt5_26111.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt5_26111/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tt5_26111/09_2025/7tt5_26111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt5_26111/09_2025/7tt5_26111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tt5_26111/09_2025/7tt5_26111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt5_26111/09_2025/7tt5_26111.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.92, per 1000 atoms: 0.20 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: 1.19 Conformation dependent library (CDL) restraints added in 367.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.36 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: 3.18 Time building geometry restraints manager: 1.70 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: 0.990 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.400 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (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 ARG 0.017 0.002 ARG A 661 TYR 0.024 0.002 TYR A 348 PHE 0.035 0.002 PHE A 395 TRP 0.016 0.002 TRP A 546 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7482) covalent geometry : angle 0.69408 (10131) SS BOND : bond 0.00860 ( 2) SS BOND : angle 1.90727 ( 4) hydrogen bonds : bond 0.24200 ( 367) hydrogen bonds : angle 8.96895 ( 1032) *********************** 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 : 0.389 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: P 1265 ASN cc_start: 0.9638 (m-40) cc_final: 0.9435 (p0) REVERT: P 1296 PHE cc_start: 0.9284 (t80) cc_final: 0.8768 (t80) REVERT: A 306 ASP cc_start: 0.9382 (m-30) cc_final: 0.8933 (p0) REVERT: A 307 ASP cc_start: 0.9283 (m-30) cc_final: 0.8933 (m-30) REVERT: A 372 MET cc_start: 0.8203 (mmp) cc_final: 0.7699 (mmm) REVERT: A 386 LYS cc_start: 0.9361 (tttt) cc_final: 0.9115 (ttpt) REVERT: A 388 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8436 (tpp-160) REVERT: A 440 PHE cc_start: 0.8256 (m-80) cc_final: 0.7858 (m-10) REVERT: A 474 THR cc_start: 0.9117 (m) cc_final: 0.8846 (p) REVERT: A 491 TYR cc_start: 0.8490 (t80) cc_final: 0.8159 (t80) REVERT: A 535 SER cc_start: 0.7688 (t) cc_final: 0.7399 (t) REVERT: A 582 ASP cc_start: 0.8688 (p0) cc_final: 0.8209 (t70) REVERT: A 637 TYR cc_start: 0.8225 (t80) cc_final: 0.7885 (t80) REVERT: A 645 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7759 (tp30) REVERT: A 711 MET cc_start: 0.8728 (ppp) cc_final: 0.8126 (ppp) REVERT: A 741 MET cc_start: 0.8245 (pmm) cc_final: 0.7758 (pmm) REVERT: A 765 ASN cc_start: 0.9266 (m-40) cc_final: 0.8930 (m-40) REVERT: E 27 VAL cc_start: 0.9545 (t) cc_final: 0.9263 (m) REVERT: E 42 ASP cc_start: 0.9189 (m-30) cc_final: 0.8782 (m-30) REVERT: E 80 GLN cc_start: 0.8881 (tt0) cc_final: 0.8569 (tp-100) REVERT: E 84 GLU cc_start: 0.8532 (tp30) cc_final: 0.8258 (mm-30) REVERT: E 90 THR cc_start: 0.8901 (m) cc_final: 0.8374 (m) REVERT: D 84 ASP cc_start: 0.8424 (m-30) cc_final: 0.8000 (t0) REVERT: D 87 LEU cc_start: 0.9333 (mt) cc_final: 0.9013 (mt) REVERT: D 131 ASP cc_start: 0.7846 (t0) cc_final: 0.7615 (t0) REVERT: D 136 ASP cc_start: 0.9341 (t0) cc_final: 0.8244 (t0) REVERT: D 213 ASP cc_start: 0.8557 (m-30) cc_final: 0.8163 (t70) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2309 time to fit residues: 89.5333 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 : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1062 HIS A 445 GLN D 82 ASN D 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094830 restraints weight = 40627.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099097 restraints weight = 19248.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101797 restraints weight = 12437.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103238 restraints weight = 9707.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104308 restraints weight = 8533.424| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 7484 Z= 0.244 Angle : 0.648 14.803 10135 Z= 0.369 Chirality : 0.044 0.173 1065 Planarity : 0.005 0.063 1325 Dihedral : 4.641 43.015 1018 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.28), residues: 890 helix: 1.18 (0.37), residues: 198 sheet: 0.85 (0.26), residues: 355 loop : 0.79 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P1269 TYR 0.027 0.002 TYR A 550 PHE 0.020 0.002 PHE A 395 TRP 0.012 0.001 TRP A 546 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 7482) covalent geometry : angle 0.64009 (10131) SS BOND : bond 0.01627 ( 2) SS BOND : angle 5.13187 ( 4) hydrogen bonds : bond 0.04819 ( 367) hydrogen bonds : angle 6.81326 ( 1032) *********************** 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 234 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.386 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: P 1271 ASN cc_start: 0.8451 (p0) cc_final: 0.8219 (p0) REVERT: A 304 MET cc_start: 0.8466 (pmm) cc_final: 0.8247 (pmm) REVERT: A 386 LYS cc_start: 0.9370 (tttt) cc_final: 0.9098 (ttpt) REVERT: A 408 SER cc_start: 0.8958 (t) cc_final: 0.8735 (t) REVERT: A 474 THR cc_start: 0.9079 (m) cc_final: 0.8799 (p) REVERT: A 637 TYR cc_start: 0.8282 (t80) cc_final: 0.7676 (t80) REVERT: A 645 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7794 (tp30) REVERT: A 711 MET cc_start: 0.8803 (ppp) cc_final: 0.8550 (ppp) REVERT: A 738 PHE cc_start: 0.8911 (p90) cc_final: 0.8693 (p90) REVERT: A 741 MET cc_start: 0.8055 (pmm) cc_final: 0.7621 (pmm) REVERT: A 765 ASN cc_start: 0.9353 (m-40) cc_final: 0.9103 (m-40) REVERT: E 46 ILE cc_start: 0.9064 (mm) cc_final: 0.8857 (mp) REVERT: E 83 HIS cc_start: 0.8284 (p-80) cc_final: 0.7793 (p90) REVERT: E 105 ASP cc_start: 0.7334 (m-30) cc_final: 0.6974 (m-30) REVERT: D 87 LEU cc_start: 0.9524 (mt) cc_final: 0.9121 (mt) REVERT: D 213 ASP cc_start: 0.8440 (m-30) cc_final: 0.8116 (t70) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1986 time to fit residues: 60.9231 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 : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1086 HIS D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.094472 restraints weight = 41009.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098885 restraints weight = 19491.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101696 restraints weight = 12687.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.103274 restraints weight = 9939.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104411 restraints weight = 8703.515| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7484 Z= 0.140 Angle : 0.535 10.864 10135 Z= 0.301 Chirality : 0.042 0.162 1065 Planarity : 0.004 0.055 1325 Dihedral : 4.527 48.288 1018 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.13 % Allowed : 0.92 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.28), residues: 890 helix: 1.54 (0.37), residues: 199 sheet: 0.61 (0.26), residues: 353 loop : 0.66 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 321 TYR 0.016 0.001 TYR A 550 PHE 0.014 0.001 PHE A 718 TRP 0.007 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7482) covalent geometry : angle 0.53089 (10131) SS BOND : bond 0.01081 ( 2) SS BOND : angle 3.24819 ( 4) hydrogen bonds : bond 0.03953 ( 367) hydrogen bonds : angle 6.10914 ( 1032) *********************** 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 230 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.315 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: P 1271 ASN cc_start: 0.8512 (p0) cc_final: 0.8237 (p0) REVERT: A 352 ILE cc_start: 0.9133 (mt) cc_final: 0.8178 (mt) REVERT: A 386 LYS cc_start: 0.9339 (tttt) cc_final: 0.8995 (ttpt) REVERT: A 408 SER cc_start: 0.9106 (t) cc_final: 0.8875 (t) REVERT: A 474 THR cc_start: 0.9067 (m) cc_final: 0.8787 (p) REVERT: A 582 ASP cc_start: 0.9059 (p0) cc_final: 0.8405 (t0) REVERT: A 609 TYR cc_start: 0.8490 (p90) cc_final: 0.8278 (p90) REVERT: A 614 ASP cc_start: 0.8727 (t70) cc_final: 0.8398 (t0) REVERT: A 637 TYR cc_start: 0.8240 (t80) cc_final: 0.7840 (t80) REVERT: A 645 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7909 (tp30) REVERT: A 711 MET cc_start: 0.8873 (ppp) cc_final: 0.8225 (ppp) REVERT: A 741 MET cc_start: 0.8018 (pmm) cc_final: 0.7566 (pmm) REVERT: E 46 ILE cc_start: 0.9031 (mm) cc_final: 0.8807 (mp) REVERT: E 105 ASP cc_start: 0.7179 (m-30) cc_final: 0.6846 (m-30) REVERT: D 84 ASP cc_start: 0.8077 (t0) cc_final: 0.7604 (t0) REVERT: D 213 ASP cc_start: 0.8386 (m-30) cc_final: 0.7998 (t70) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1984 time to fit residues: 59.4819 Evaluate side-chains 191 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096088 restraints weight = 40694.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100458 restraints weight = 19264.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103259 restraints weight = 12471.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104908 restraints weight = 9732.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105916 restraints weight = 8472.187| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7484 Z= 0.099 Angle : 0.493 8.130 10135 Z= 0.272 Chirality : 0.042 0.154 1065 Planarity : 0.004 0.051 1325 Dihedral : 4.440 49.843 1018 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.28), residues: 890 helix: 1.70 (0.37), residues: 199 sheet: 0.51 (0.27), residues: 342 loop : 0.61 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 321 TYR 0.014 0.001 TYR A 550 PHE 0.011 0.001 PHE A 395 TRP 0.007 0.001 TRP D 191 HIS 0.006 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 7482) covalent geometry : angle 0.49088 (10131) SS BOND : bond 0.00906 ( 2) SS BOND : angle 2.32710 ( 4) hydrogen bonds : bond 0.03314 ( 367) hydrogen bonds : angle 5.62176 ( 1032) *********************** 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 222 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.417 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: P 1112 MET cc_start: 0.8876 (ppp) cc_final: 0.8486 (pmm) REVERT: P 1159 TYR cc_start: 0.8545 (t80) cc_final: 0.8166 (t80) REVERT: P 1217 LYS cc_start: 0.9187 (tptp) cc_final: 0.8855 (mptt) REVERT: A 304 MET cc_start: 0.8394 (pmm) cc_final: 0.8011 (pmm) REVERT: A 386 LYS cc_start: 0.9306 (tttt) cc_final: 0.8972 (ttpt) REVERT: A 474 THR cc_start: 0.9102 (m) cc_final: 0.8777 (p) REVERT: A 582 ASP cc_start: 0.9042 (p0) cc_final: 0.8342 (t0) REVERT: A 614 ASP cc_start: 0.8731 (t70) cc_final: 0.8442 (t0) REVERT: A 637 TYR cc_start: 0.8263 (t80) cc_final: 0.7847 (t80) REVERT: A 711 MET cc_start: 0.8915 (ppp) cc_final: 0.8211 (ppp) REVERT: A 741 MET cc_start: 0.8072 (pmm) cc_final: 0.7638 (pmm) REVERT: A 765 ASN cc_start: 0.9076 (m110) cc_final: 0.8856 (m-40) REVERT: E 46 ILE cc_start: 0.9021 (mm) cc_final: 0.8747 (mp) REVERT: E 105 ASP cc_start: 0.6930 (m-30) cc_final: 0.6643 (m-30) REVERT: D 84 ASP cc_start: 0.8105 (t0) cc_final: 0.7647 (t0) REVERT: D 136 ASP cc_start: 0.8879 (t0) cc_final: 0.8646 (t0) REVERT: D 199 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7906 (tm-30) REVERT: D 204 ASP cc_start: 0.8735 (p0) cc_final: 0.8372 (p0) REVERT: D 213 ASP cc_start: 0.8274 (m-30) cc_final: 0.7923 (t70) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2103 time to fit residues: 60.7255 Evaluate side-chains 191 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.138351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.087256 restraints weight = 43545.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091789 restraints weight = 19963.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.094594 restraints weight = 12798.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096353 restraints weight = 10010.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.097215 restraints weight = 8695.746| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 7484 Z= 0.178 Angle : 0.595 22.186 10135 Z= 0.323 Chirality : 0.043 0.371 1065 Planarity : 0.004 0.055 1325 Dihedral : 4.713 49.993 1018 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.28), residues: 890 helix: 1.43 (0.37), residues: 199 sheet: 0.24 (0.26), residues: 348 loop : 0.33 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 321 TYR 0.016 0.001 TYR D 205 PHE 0.016 0.002 PHE A 648 TRP 0.009 0.001 TRP D 48 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7482) covalent geometry : angle 0.58290 (10131) SS BOND : bond 0.01510 ( 2) SS BOND : angle 6.02252 ( 4) hydrogen bonds : bond 0.03549 ( 367) hydrogen bonds : angle 5.62201 ( 1032) *********************** 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: 0 poor density : 211 time to evaluate : 0.389 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: 0.9142 (ppp) cc_final: 0.8767 (pmm) REVERT: P 1159 TYR cc_start: 0.8819 (t80) cc_final: 0.8355 (t80) REVERT: P 1217 LYS cc_start: 0.9313 (tptp) cc_final: 0.8918 (mptt) REVERT: A 386 LYS cc_start: 0.9363 (tttt) cc_final: 0.9057 (ttpt) REVERT: A 445 GLN cc_start: 0.8780 (pt0) cc_final: 0.8056 (pp30) REVERT: A 474 THR cc_start: 0.9170 (m) cc_final: 0.8905 (p) REVERT: A 614 ASP cc_start: 0.8833 (t70) cc_final: 0.8622 (t0) REVERT: A 645 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 711 MET cc_start: 0.8951 (ppp) cc_final: 0.8301 (ppp) REVERT: E 46 ILE cc_start: 0.9158 (mm) cc_final: 0.8878 (mp) REVERT: E 104 ILE cc_start: 0.8818 (mt) cc_final: 0.8616 (mt) REVERT: E 105 ASP cc_start: 0.7149 (m-30) cc_final: 0.5978 (m-30) REVERT: D 84 ASP cc_start: 0.8041 (t0) cc_final: 0.7576 (t0) REVERT: D 199 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8019 (tm-30) REVERT: D 213 ASP cc_start: 0.8481 (m-30) cc_final: 0.8042 (t70) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2104 time to fit residues: 58.1539 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.088835 restraints weight = 42709.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093410 restraints weight = 19357.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096319 restraints weight = 12408.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098041 restraints weight = 9668.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098808 restraints weight = 8418.921| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7484 Z= 0.126 Angle : 0.529 12.644 10135 Z= 0.291 Chirality : 0.043 0.254 1065 Planarity : 0.004 0.054 1325 Dihedral : 4.797 53.559 1018 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.28), residues: 890 helix: 1.49 (0.37), residues: 199 sheet: 0.18 (0.27), residues: 338 loop : 0.35 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P1269 TYR 0.025 0.001 TYR A 550 PHE 0.017 0.001 PHE E 74 TRP 0.007 0.001 TRP D 48 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7482) covalent geometry : angle 0.52014 (10131) SS BOND : bond 0.00594 ( 2) SS BOND : angle 4.93037 ( 4) hydrogen bonds : bond 0.03255 ( 367) hydrogen bonds : angle 5.42794 ( 1032) *********************** 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 210 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.332 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: P 1112 MET cc_start: 0.9214 (ppp) cc_final: 0.8874 (pmm) REVERT: P 1159 TYR cc_start: 0.8834 (t80) cc_final: 0.8365 (t80) REVERT: P 1217 LYS cc_start: 0.9292 (tptp) cc_final: 0.8907 (mptt) REVERT: A 307 ASP cc_start: 0.9066 (m-30) cc_final: 0.8859 (m-30) REVERT: A 386 LYS cc_start: 0.9381 (tttt) cc_final: 0.9073 (ttpt) REVERT: A 430 ILE cc_start: 0.8367 (pt) cc_final: 0.7818 (tp) REVERT: A 440 PHE cc_start: 0.8498 (m-80) cc_final: 0.7945 (m-10) REVERT: A 474 THR cc_start: 0.9139 (m) cc_final: 0.8891 (p) REVERT: A 645 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7825 (tp30) REVERT: A 711 MET cc_start: 0.8982 (ppp) cc_final: 0.8301 (ppp) REVERT: E 46 ILE cc_start: 0.9144 (mm) cc_final: 0.8828 (mp) REVERT: E 88 GLN cc_start: 0.7772 (pp30) cc_final: 0.7535 (pp30) REVERT: E 105 ASP cc_start: 0.6886 (m-30) cc_final: 0.5833 (m-30) REVERT: E 110 LEU cc_start: 0.8474 (tp) cc_final: 0.8268 (tp) REVERT: D 53 THR cc_start: 0.8979 (m) cc_final: 0.8746 (p) REVERT: D 84 ASP cc_start: 0.7976 (t0) cc_final: 0.7483 (t0) REVERT: D 199 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 213 ASP cc_start: 0.8464 (m-30) cc_final: 0.8027 (t70) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2055 time to fit residues: 56.9877 Evaluate side-chains 180 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.090029 restraints weight = 43211.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094838 restraints weight = 19669.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097908 restraints weight = 12489.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099535 restraints weight = 9642.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100774 restraints weight = 8418.470| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7484 Z= 0.102 Angle : 0.491 9.576 10135 Z= 0.268 Chirality : 0.042 0.233 1065 Planarity : 0.004 0.060 1325 Dihedral : 4.571 44.202 1018 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.28), residues: 890 helix: 1.72 (0.37), residues: 199 sheet: 0.21 (0.27), residues: 335 loop : 0.40 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P1269 TYR 0.019 0.001 TYR A 550 PHE 0.013 0.001 PHE A 648 TRP 0.010 0.001 TRP D 191 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7482) covalent geometry : angle 0.48492 (10131) SS BOND : bond 0.00469 ( 2) SS BOND : angle 3.87067 ( 4) hydrogen bonds : bond 0.03028 ( 367) hydrogen bonds : angle 5.15110 ( 1032) *********************** 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 209 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.410 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: P 1112 MET cc_start: 0.9222 (ppp) cc_final: 0.8893 (pmm) REVERT: P 1159 TYR cc_start: 0.8861 (t80) cc_final: 0.8390 (t80) REVERT: A 307 ASP cc_start: 0.9053 (m-30) cc_final: 0.8831 (m-30) REVERT: A 386 LYS cc_start: 0.9360 (tttt) cc_final: 0.9036 (ttpt) REVERT: A 440 PHE cc_start: 0.8496 (m-80) cc_final: 0.8255 (m-80) REVERT: A 474 THR cc_start: 0.9150 (m) cc_final: 0.8891 (p) REVERT: A 711 MET cc_start: 0.8984 (ppp) cc_final: 0.8314 (ppp) REVERT: E 46 ILE cc_start: 0.9163 (mm) cc_final: 0.8797 (mp) REVERT: E 91 LEU cc_start: 0.9374 (tp) cc_final: 0.9160 (tp) REVERT: E 105 ASP cc_start: 0.6866 (m-30) cc_final: 0.5905 (m-30) REVERT: D 84 ASP cc_start: 0.8011 (t0) cc_final: 0.7527 (t0) REVERT: D 149 LYS cc_start: 0.8863 (mmpt) cc_final: 0.8470 (tppt) REVERT: D 199 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7986 (tm-30) REVERT: D 213 ASP cc_start: 0.8516 (m-30) cc_final: 0.8020 (t70) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2032 time to fit residues: 55.9737 Evaluate side-chains 193 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.139736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.088792 restraints weight = 42928.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093483 restraints weight = 19618.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096501 restraints weight = 12507.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.098287 restraints weight = 9677.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099201 restraints weight = 8399.962| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7484 Z= 0.124 Angle : 0.500 7.570 10135 Z= 0.270 Chirality : 0.041 0.225 1065 Planarity : 0.004 0.043 1325 Dihedral : 4.571 43.834 1018 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.28), residues: 890 helix: 1.67 (0.37), residues: 199 sheet: 0.12 (0.26), residues: 337 loop : 0.39 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P1297 TYR 0.016 0.001 TYR A 550 PHE 0.017 0.001 PHE P1300 TRP 0.008 0.001 TRP D 191 HIS 0.006 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7482) covalent geometry : angle 0.49573 (10131) SS BOND : bond 0.00280 ( 2) SS BOND : angle 3.18870 ( 4) hydrogen bonds : bond 0.03027 ( 367) hydrogen bonds : angle 5.09822 ( 1032) *********************** 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 211 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.356 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: P 1112 MET cc_start: 0.9157 (ppp) cc_final: 0.8857 (pmm) REVERT: P 1159 TYR cc_start: 0.8855 (t80) cc_final: 0.8392 (t80) REVERT: A 307 ASP cc_start: 0.9042 (m-30) cc_final: 0.8818 (m-30) REVERT: A 386 LYS cc_start: 0.9384 (tttt) cc_final: 0.9063 (ttpt) REVERT: A 703 ASP cc_start: 0.8376 (p0) cc_final: 0.8008 (p0) REVERT: A 711 MET cc_start: 0.8975 (ppp) cc_final: 0.8569 (ppp) REVERT: A 765 ASN cc_start: 0.9149 (m110) cc_final: 0.8777 (m-40) REVERT: E 46 ILE cc_start: 0.9156 (mm) cc_final: 0.8874 (mp) REVERT: E 105 ASP cc_start: 0.6952 (m-30) cc_final: 0.5930 (m-30) REVERT: D 53 THR cc_start: 0.9012 (m) cc_final: 0.8698 (p) REVERT: D 84 ASP cc_start: 0.8038 (t0) cc_final: 0.7571 (t0) REVERT: D 149 LYS cc_start: 0.8862 (mmpt) cc_final: 0.8471 (tppt) REVERT: D 199 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8005 (tm-30) REVERT: D 213 ASP cc_start: 0.8431 (m-30) cc_final: 0.8006 (t70) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1999 time to fit residues: 55.3778 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 : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 40.0000 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.085984 restraints weight = 43454.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.090392 restraints weight = 20235.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093245 restraints weight = 13169.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094936 restraints weight = 10287.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095805 restraints weight = 8969.227| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7484 Z= 0.206 Angle : 0.547 7.437 10135 Z= 0.305 Chirality : 0.042 0.239 1065 Planarity : 0.004 0.051 1325 Dihedral : 4.828 42.681 1018 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.27), residues: 890 helix: 1.24 (0.36), residues: 199 sheet: -0.02 (0.26), residues: 349 loop : -0.03 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 366 TYR 0.015 0.001 TYR E 75 PHE 0.024 0.002 PHE A 802 TRP 0.007 0.001 TRP A 749 HIS 0.006 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 7482) covalent geometry : angle 0.54333 (10131) SS BOND : bond 0.00271 ( 2) SS BOND : angle 3.23295 ( 4) hydrogen bonds : bond 0.03456 ( 367) hydrogen bonds : angle 5.32755 ( 1032) *********************** 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 198 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.298 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: 0.9197 (ppp) cc_final: 0.8906 (pmm) REVERT: P 1159 TYR cc_start: 0.8898 (t80) cc_final: 0.8561 (t80) REVERT: A 307 ASP cc_start: 0.9045 (m-30) cc_final: 0.8835 (m-30) REVERT: A 386 LYS cc_start: 0.9410 (tttt) cc_final: 0.9134 (ttpt) REVERT: A 445 GLN cc_start: 0.8839 (pt0) cc_final: 0.8144 (pp30) REVERT: A 645 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 711 MET cc_start: 0.8980 (ppp) cc_final: 0.8321 (ppp) REVERT: A 740 ASP cc_start: 0.8753 (m-30) cc_final: 0.8522 (m-30) REVERT: A 741 MET cc_start: 0.7971 (pmm) cc_final: 0.7380 (pmm) REVERT: A 765 ASN cc_start: 0.9265 (m110) cc_final: 0.8885 (m-40) REVERT: E 46 ILE cc_start: 0.9182 (mm) cc_final: 0.8852 (mp) REVERT: E 88 GLN cc_start: 0.7874 (pp30) cc_final: 0.7636 (pp30) REVERT: E 105 ASP cc_start: 0.6819 (m-30) cc_final: 0.5775 (m-30) REVERT: D 53 THR cc_start: 0.9048 (m) cc_final: 0.8739 (p) REVERT: D 84 ASP cc_start: 0.8176 (t0) cc_final: 0.7746 (t0) REVERT: D 136 ASP cc_start: 0.8957 (t0) cc_final: 0.8737 (t0) REVERT: D 213 ASP cc_start: 0.8464 (m-30) cc_final: 0.8086 (t70) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2070 time to fit residues: 53.5844 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 : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.092829 restraints weight = 41525.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.097073 restraints weight = 20430.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099742 restraints weight = 13495.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101182 restraints weight = 10689.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102325 restraints weight = 9413.183| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7484 Z= 0.112 Angle : 0.518 8.321 10135 Z= 0.279 Chirality : 0.042 0.217 1065 Planarity : 0.004 0.057 1325 Dihedral : 4.693 41.802 1018 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.28), residues: 890 helix: 1.51 (0.36), residues: 199 sheet: -0.01 (0.26), residues: 347 loop : 0.16 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG P1158 TYR 0.014 0.001 TYR A 550 PHE 0.019 0.001 PHE P1300 TRP 0.015 0.001 TRP P1166 HIS 0.006 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7482) covalent geometry : angle 0.51569 (10131) SS BOND : bond 0.00212 ( 2) SS BOND : angle 2.69527 ( 4) hydrogen bonds : bond 0.03034 ( 367) hydrogen bonds : angle 5.08130 ( 1032) ********************** 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 200 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.384 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: 0.9114 (ppp) cc_final: 0.8852 (pmm) REVERT: P 1159 TYR cc_start: 0.8671 (t80) cc_final: 0.8195 (t80) REVERT: P 1296 PHE cc_start: 0.8699 (t80) cc_final: 0.8447 (t80) REVERT: A 372 MET cc_start: 0.7814 (mmm) cc_final: 0.7501 (mmp) REVERT: A 373 GLU cc_start: 0.7733 (mp0) cc_final: 0.7254 (mt-10) REVERT: A 386 LYS cc_start: 0.9355 (tttt) cc_final: 0.9071 (ttpt) REVERT: A 445 GLN cc_start: 0.8686 (pt0) cc_final: 0.8044 (pp30) REVERT: A 639 ASP cc_start: 0.7680 (t0) cc_final: 0.7428 (t0) REVERT: A 645 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7435 (mm-30) REVERT: A 711 MET cc_start: 0.9002 (ppp) cc_final: 0.8325 (ppp) REVERT: A 765 ASN cc_start: 0.9148 (m110) cc_final: 0.8742 (m-40) REVERT: E 46 ILE cc_start: 0.9106 (mm) cc_final: 0.8743 (mp) REVERT: E 105 ASP cc_start: 0.6660 (m-30) cc_final: 0.5728 (m-30) REVERT: D 53 THR cc_start: 0.9054 (m) cc_final: 0.8750 (p) REVERT: D 79 TYR cc_start: 0.7950 (m-10) cc_final: 0.7666 (m-10) REVERT: D 136 ASP cc_start: 0.8897 (t0) cc_final: 0.8681 (t0) REVERT: D 149 LYS cc_start: 0.8817 (mmpt) cc_final: 0.8373 (tppt) REVERT: D 213 ASP cc_start: 0.8392 (m-30) cc_final: 0.7961 (t70) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1895 time to fit residues: 50.7413 Evaluate side-chains 176 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 0 optimal weight: 80.0000 chunk 17 optimal weight: 0.0970 chunk 25 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.088588 restraints weight = 42953.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.093161 restraints weight = 19928.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096092 restraints weight = 12877.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097869 restraints weight = 10032.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098644 restraints weight = 8725.812| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7484 Z= 0.105 Angle : 0.503 7.097 10135 Z= 0.273 Chirality : 0.042 0.176 1065 Planarity : 0.004 0.044 1325 Dihedral : 4.579 39.593 1018 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.28), residues: 890 helix: 1.58 (0.37), residues: 199 sheet: -0.02 (0.26), residues: 347 loop : 0.21 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P1158 TYR 0.017 0.001 TYR P1298 PHE 0.025 0.001 PHE A 426 TRP 0.009 0.001 TRP P1166 HIS 0.006 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7482) covalent geometry : angle 0.50161 (10131) SS BOND : bond 0.00229 ( 2) SS BOND : angle 1.73657 ( 4) hydrogen bonds : bond 0.03132 ( 367) hydrogen bonds : angle 4.91019 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2986.08 seconds wall clock time: 51 minutes 23.42 seconds (3083.42 seconds total)