Starting phenix.real_space_refine on Wed Aug 5 03:40:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vbe_43122/08_2026/8vbe_43122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vbe_43122/08_2026/8vbe_43122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vbe_43122/08_2026/8vbe_43122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vbe_43122/08_2026/8vbe_43122.map" model { file = "/net/cci-nas-00/data/ceres_data/8vbe_43122/08_2026/8vbe_43122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vbe_43122/08_2026/8vbe_43122.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 42 5.49 5 Mg 2 5.21 5 S 14 5.16 5 C 5312 2.51 5 N 1407 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8421 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4384 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 500} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3203 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 28, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 802 Classifications: {'DNA': 37, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 38} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.75, per 1000 atoms: 0.21 Number of scatterers: 8421 At special positions: 0 Unit cell: (80.025, 95.7, 122.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 42 15.00 Mg 2 11.99 O 1644 8.00 N 1407 7.00 C 5312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 343.8 milliseconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 37.8% alpha, 15.8% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 removed outlier: 3.598A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.471A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 129 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix removed outlier: 3.596A pdb=" N GLN A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.644A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.557A pdb=" N GLU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 384 removed outlier: 3.718A pdb=" N GLN A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 removed outlier: 4.057A pdb=" N GLU A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.870A pdb=" N THR A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.661A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.509A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.767A pdb=" N ASN B 81 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 83' Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.700A pdb=" N PHE B 116 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 156 through 165 removed outlier: 5.469A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 253 through 271 removed outlier: 3.613A pdb=" N LYS B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.776A pdb=" N ARG B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 363 through 382 removed outlier: 3.909A pdb=" N GLN B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.556A pdb=" N ILE A 142 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 354 removed outlier: 8.621A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 447 removed outlier: 3.786A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 497 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB2, first strand: chain 'B' and resid 105 through 110 Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 355 removed outlier: 8.581A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1392 1.32 - 1.45: 2403 1.45 - 1.57: 4819 1.57 - 1.69: 82 1.69 - 1.81: 24 Bond restraints: 8720 Sorted by residual: bond pdb=" N ILE A 132 " pdb=" CA ILE A 132 " ideal model delta sigma weight residual 1.460 1.490 -0.030 7.60e-03 1.73e+04 1.56e+01 bond pdb=" C ASP A 110 " pdb=" N VAL A 111 " ideal model delta sigma weight residual 1.329 1.271 0.058 1.69e-02 3.50e+03 1.19e+01 bond pdb=" N VAL B 381 " pdb=" CA VAL B 381 " ideal model delta sigma weight residual 1.461 1.502 -0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ILE A 380 " pdb=" CA ILE A 380 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.64e+00 ... (remaining 8715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 11570 1.64 - 3.29: 371 3.29 - 4.93: 66 4.93 - 6.58: 7 6.58 - 8.22: 7 Bond angle restraints: 12021 Sorted by residual: angle pdb=" CA ILE B 382 " pdb=" C ILE B 382 " pdb=" O ILE B 382 " ideal model delta sigma weight residual 121.68 116.33 5.35 7.90e-01 1.60e+00 4.58e+01 angle pdb=" C ILE A 382 " pdb=" N TRP A 383 " pdb=" CA TRP A 383 " ideal model delta sigma weight residual 122.23 114.01 8.22 1.57e+00 4.06e-01 2.74e+01 angle pdb=" PB DTP A 601 " pdb=" O3B DTP A 601 " pdb=" PG DTP A 601 " ideal model delta sigma weight residual 139.87 135.45 4.42 1.00e+00 1.00e+00 1.96e+01 angle pdb=" O4' DA F 34 " pdb=" C4' DA F 34 " pdb=" C3' DA F 34 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" C3' DG F 14 " pdb=" O3' DG F 14 " pdb=" P DC F 15 " ideal model delta sigma weight residual 119.70 124.79 -5.09 1.20e+00 6.94e-01 1.80e+01 ... (remaining 12016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.96: 4617 27.96 - 55.93: 466 55.93 - 83.89: 48 83.89 - 111.86: 4 111.86 - 139.82: 1 Dihedral angle restraints: 5136 sinusoidal: 2411 harmonic: 2725 Sorted by residual: dihedral pdb=" O1B DTP A 601 " pdb=" O3B DTP A 601 " pdb=" PB DTP A 601 " pdb=" PG DTP A 601 " ideal model delta sinusoidal sigma weight residual 299.93 160.11 139.82 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" CA VAL B 10 " pdb=" C VAL B 10 " pdb=" N LYS B 11 " pdb=" CA LYS B 11 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CB GLU B 203 " pdb=" CG GLU B 203 " pdb=" CD GLU B 203 " pdb=" OE1 GLU B 203 " ideal model delta sinusoidal sigma weight residual 0.00 89.60 -89.60 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1028 0.053 - 0.106: 238 0.106 - 0.158: 43 0.158 - 0.211: 5 0.211 - 0.264: 1 Chirality restraints: 1315 Sorted by residual: chirality pdb=" CA ILE B 382 " pdb=" N ILE B 382 " pdb=" C ILE B 382 " pdb=" CB ILE B 382 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE A 132 " pdb=" N ILE A 132 " pdb=" C ILE A 132 " pdb=" CB ILE A 132 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DA F 34 " pdb=" C4' DA F 34 " pdb=" O3' DA F 34 " pdb=" C2' DA F 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1312 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 379 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C SER A 379 " 0.045 2.00e-02 2.50e+03 pdb=" O SER A 379 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 380 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 107 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C THR A 107 " -0.038 2.00e-02 2.50e+03 pdb=" O THR A 107 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 108 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA F 34 " -0.026 2.00e-02 2.50e+03 1.16e-02 3.69e+00 pdb=" N9 DA F 34 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA F 34 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA F 34 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA F 34 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA F 34 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA F 34 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA F 34 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA F 34 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA F 34 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA F 34 " 0.006 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 89 2.62 - 3.19: 6581 3.19 - 3.76: 12891 3.76 - 4.33: 18087 4.33 - 4.90: 29498 Nonbonded interactions: 67146 Sorted by model distance: nonbonded pdb=" O VAL A 111 " pdb="MG MG A 602 " model vdw 2.052 2.170 nonbonded pdb=" O1A DTP A 601 " pdb="MG MG A 602 " model vdw 2.128 2.170 nonbonded pdb=" O ARG B 356 " pdb=" NH1 ARG B 356 " model vdw 2.129 3.120 nonbonded pdb=" NZ LYS B 172 " pdb=" O ILE B 178 " model vdw 2.200 3.120 nonbonded pdb=" OD2 ASP A 185 " pdb="MG MG A 602 " model vdw 2.287 2.170 ... (remaining 67141 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.090 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 0.058 8720 Z= 0.275 Angle : 0.698 8.222 12021 Z= 0.467 Chirality : 0.047 0.264 1315 Planarity : 0.005 0.047 1372 Dihedral : 19.817 139.825 3376 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.01 % Favored : 95.45 % Rotamer: Outliers : 4.46 % Allowed : 20.99 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: -0.35 (0.28), residues: 923 helix: 1.03 (0.32), residues: 309 sheet: 0.06 (0.38), residues: 188 loop : -1.33 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 277 TYR 0.010 0.001 TYR A 501 PHE 0.008 0.001 PHE B 61 TRP 0.012 0.001 TRP B 410 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.27 ( 8720) covalent geometry : angle 0.69754 / 0.47 (12021) hydrogen bonds : bond 0.17766 / 11.56 ( 335) hydrogen bonds : angle 5.58432 / 4.11 ( 871) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 51 time to evaluate : 0.255 Fit side-chains REVERT: B 113 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: B 166 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5560 (pttm) REVERT: B 277 ARG cc_start: 0.7553 (ttp80) cc_final: 0.6950 (ttp80) REVERT: B 281 LYS cc_start: 0.7452 (ttmt) cc_final: 0.7029 (mtmm) outliers start: 37 outliers final: 27 residues processed: 86 average time/residue: 0.5154 time to fit residues: 47.1061 Evaluate side-chains 77 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN B 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098079 restraints weight = 12735.394| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.34 r_work: 0.3158 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8720 Z= 0.263 Angle : 0.662 10.663 12021 Z= 0.359 Chirality : 0.048 0.267 1315 Planarity : 0.005 0.039 1372 Dihedral : 18.771 149.249 1475 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.55 % Favored : 94.91 % Rotamer: Outliers : 5.55 % Allowed : 19.66 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: -0.57 (0.27), residues: 923 helix: 0.87 (0.31), residues: 312 sheet: -0.16 (0.37), residues: 186 loop : -1.43 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 358 TYR 0.013 0.002 TYR B 271 PHE 0.012 0.002 PHE A 160 TRP 0.013 0.002 TRP A 88 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.26 ( 8720) covalent geometry : angle 0.66240 / 0.36 (12021) hydrogen bonds : bond 0.05951 / 3.82 ( 335) hydrogen bonds : angle 4.61478 / 3.30 ( 871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 53 time to evaluate : 0.311 Fit side-chains REVERT: A 50 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.7978 (mp) REVERT: A 413 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: A 500 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: B 275 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6340 (mtmm) REVERT: B 374 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7631 (mmmt) outliers start: 46 outliers final: 26 residues processed: 94 average time/residue: 0.5982 time to fit residues: 59.8042 Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN A 373 GLN B 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100588 restraints weight = 12590.501| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.31 r_work: 0.3197 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8720 Z= 0.138 Angle : 0.561 7.766 12021 Z= 0.307 Chirality : 0.044 0.251 1315 Planarity : 0.004 0.040 1372 Dihedral : 18.379 157.187 1458 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.12 % Favored : 95.45 % Rotamer: Outliers : 5.07 % Allowed : 20.14 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: -0.27 (0.28), residues: 923 helix: 1.25 (0.32), residues: 312 sheet: -0.01 (0.37), residues: 186 loop : -1.36 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 358 TYR 0.012 0.001 TYR A 501 PHE 0.009 0.001 PHE B 61 TRP 0.011 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 8720) covalent geometry : angle 0.56071 / 0.31 (12021) hydrogen bonds : bond 0.04400 / 2.86 ( 335) hydrogen bonds : angle 4.29357 / 3.06 ( 871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 53 time to evaluate : 0.372 Fit side-chains REVERT: A 50 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8092 (mp) REVERT: A 500 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: B 277 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7125 (ttp80) REVERT: B 281 LYS cc_start: 0.7209 (ttmt) cc_final: 0.7003 (ttmt) outliers start: 42 outliers final: 24 residues processed: 88 average time/residue: 0.5620 time to fit residues: 52.5543 Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101687 restraints weight = 12804.604| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.36 r_work: 0.3215 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8720 Z= 0.120 Angle : 0.528 8.379 12021 Z= 0.289 Chirality : 0.043 0.225 1315 Planarity : 0.004 0.041 1372 Dihedral : 17.919 165.089 1451 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.90 % Favored : 95.67 % Rotamer: Outliers : 5.19 % Allowed : 19.90 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: -0.09 (0.28), residues: 923 helix: 1.46 (0.32), residues: 312 sheet: 0.03 (0.37), residues: 188 loop : -1.29 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 284 TYR 0.011 0.001 TYR A 501 PHE 0.008 0.001 PHE B 61 TRP 0.011 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 8720) covalent geometry : angle 0.52815 / 0.29 (12021) hydrogen bonds : bond 0.03660 / 2.37 ( 335) hydrogen bonds : angle 4.09575 / 2.91 ( 871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 58 time to evaluate : 0.244 Fit side-chains REVERT: A 50 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 53 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6462 (pp20) REVERT: B 156 SER cc_start: 0.6617 (OUTLIER) cc_final: 0.6076 (m) REVERT: B 210 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6236 (tt) REVERT: B 356 ARG cc_start: 0.7445 (pmt-80) cc_final: 0.7200 (pmt-80) outliers start: 43 outliers final: 15 residues processed: 93 average time/residue: 0.5089 time to fit residues: 50.4661 Evaluate side-chains 69 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.128627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101110 restraints weight = 12777.972| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.35 r_work: 0.3209 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8720 Z= 0.126 Angle : 0.529 8.681 12021 Z= 0.287 Chirality : 0.043 0.211 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.696 164.343 1440 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.01 % Favored : 95.56 % Rotamer: Outliers : 3.98 % Allowed : 21.59 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: 0.02 (0.28), residues: 923 helix: 1.67 (0.32), residues: 304 sheet: 0.12 (0.37), residues: 186 loop : -1.27 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 277 TYR 0.011 0.001 TYR A 501 PHE 0.009 0.001 PHE B 61 TRP 0.011 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 8720) covalent geometry : angle 0.52856 / 0.29 (12021) hydrogen bonds : bond 0.03736 / 2.43 ( 335) hydrogen bonds : angle 4.01705 / 2.84 ( 871) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 0.337 Fit side-chains REVERT: A 50 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 53 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6489 (pp20) REVERT: B 156 SER cc_start: 0.6662 (OUTLIER) cc_final: 0.6170 (m) REVERT: B 210 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6238 (tt) REVERT: B 297 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6411 (mm-30) REVERT: B 356 ARG cc_start: 0.7495 (pmt-80) cc_final: 0.7243 (pmt-80) outliers start: 33 outliers final: 16 residues processed: 79 average time/residue: 0.5371 time to fit residues: 45.3428 Evaluate side-chains 73 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100032 restraints weight = 12657.694| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.33 r_work: 0.3192 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8720 Z= 0.162 Angle : 0.551 8.994 12021 Z= 0.299 Chirality : 0.044 0.201 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.750 163.456 1438 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.55 % Favored : 95.12 % Rotamer: Outliers : 4.22 % Allowed : 21.71 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: -0.03 (0.28), residues: 923 helix: 1.63 (0.32), residues: 304 sheet: 0.05 (0.37), residues: 186 loop : -1.28 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 277 TYR 0.011 0.001 TYR A 501 PHE 0.010 0.001 PHE B 61 TRP 0.011 0.001 TRP A 402 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 8720) covalent geometry : angle 0.55123 / 0.30 (12021) hydrogen bonds : bond 0.04171 / 2.71 ( 335) hydrogen bonds : angle 4.09369 / 2.90 ( 871) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.216 Fit side-chains REVERT: A 50 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8043 (mp) REVERT: B 156 SER cc_start: 0.6788 (OUTLIER) cc_final: 0.6258 (m) REVERT: B 206 ARG cc_start: 0.4475 (OUTLIER) cc_final: 0.3864 (ttp80) REVERT: B 210 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6313 (tt) REVERT: B 297 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6473 (mm-30) REVERT: B 356 ARG cc_start: 0.7524 (pmt-80) cc_final: 0.7255 (pmt-80) outliers start: 35 outliers final: 20 residues processed: 83 average time/residue: 0.5327 time to fit residues: 47.1768 Evaluate side-chains 76 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098106 restraints weight = 12921.983| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.35 r_work: 0.3160 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8720 Z= 0.223 Angle : 0.603 9.309 12021 Z= 0.326 Chirality : 0.047 0.202 1315 Planarity : 0.005 0.044 1372 Dihedral : 17.900 160.165 1437 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.88 % Favored : 94.80 % Rotamer: Outliers : 4.46 % Allowed : 21.71 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: -0.18 (0.27), residues: 923 helix: 1.47 (0.31), residues: 304 sheet: -0.09 (0.37), residues: 186 loop : -1.31 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 277 TYR 0.013 0.002 TYR A 457 PHE 0.011 0.001 PHE B 61 TRP 0.014 0.002 TRP A 406 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 ( 8720) covalent geometry : angle 0.60267 / 0.33 (12021) hydrogen bonds : bond 0.04933 / 3.20 ( 335) hydrogen bonds : angle 4.26250 / 3.03 ( 871) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 0.268 Fit side-chains REVERT: A 50 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8060 (mp) REVERT: B 156 SER cc_start: 0.6909 (OUTLIER) cc_final: 0.6306 (m) REVERT: B 206 ARG cc_start: 0.4547 (OUTLIER) cc_final: 0.3867 (ttp80) REVERT: B 210 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6437 (tt) REVERT: B 297 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6558 (mm-30) REVERT: B 356 ARG cc_start: 0.7622 (pmt-80) cc_final: 0.7339 (pmt-80) REVERT: B 374 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7585 (mmmt) outliers start: 37 outliers final: 18 residues processed: 82 average time/residue: 0.6536 time to fit residues: 56.8845 Evaluate side-chains 72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 43 optimal weight: 0.0980 chunk 41 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101036 restraints weight = 12615.423| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.34 r_work: 0.3205 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8720 Z= 0.121 Angle : 0.532 9.558 12021 Z= 0.288 Chirality : 0.043 0.232 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.774 165.449 1436 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.12 % Favored : 95.56 % Rotamer: Outliers : 3.86 % Allowed : 22.32 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: 0.12 (0.28), residues: 923 helix: 1.75 (0.32), residues: 305 sheet: 0.07 (0.38), residues: 186 loop : -1.16 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 284 TYR 0.011 0.001 TYR A 501 PHE 0.008 0.001 PHE B 61 TRP 0.025 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 8720) covalent geometry : angle 0.53164 / 0.29 (12021) hydrogen bonds : bond 0.03678 / 2.41 ( 335) hydrogen bonds : angle 4.06831 / 2.89 ( 871) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.189 Fit side-chains REVERT: A 50 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8086 (mp) REVERT: B 156 SER cc_start: 0.6800 (OUTLIER) cc_final: 0.6271 (m) REVERT: B 206 ARG cc_start: 0.4424 (OUTLIER) cc_final: 0.3801 (ttp80) REVERT: B 210 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6457 (tt) REVERT: B 356 ARG cc_start: 0.7615 (pmt-80) cc_final: 0.7344 (pmt-80) outliers start: 32 outliers final: 13 residues processed: 80 average time/residue: 0.5167 time to fit residues: 43.8738 Evaluate side-chains 69 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098524 restraints weight = 12838.641| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.35 r_work: 0.3166 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8720 Z= 0.204 Angle : 0.598 9.599 12021 Z= 0.322 Chirality : 0.046 0.260 1315 Planarity : 0.005 0.044 1372 Dihedral : 17.859 162.657 1436 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.88 % Favored : 94.80 % Rotamer: Outliers : 3.38 % Allowed : 22.68 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: -0.09 (0.27), residues: 923 helix: 1.55 (0.31), residues: 304 sheet: -0.05 (0.38), residues: 186 loop : -1.26 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 277 TYR 0.013 0.002 TYR A 457 PHE 0.011 0.001 PHE A 160 TRP 0.017 0.001 TRP A 406 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 8720) covalent geometry : angle 0.59801 / 0.32 (12021) hydrogen bonds : bond 0.04679 / 3.03 ( 335) hydrogen bonds : angle 4.18754 / 2.98 ( 871) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 49 time to evaluate : 0.256 Fit side-chains REVERT: A 50 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8061 (mp) REVERT: B 156 SER cc_start: 0.6959 (OUTLIER) cc_final: 0.6399 (m) REVERT: B 206 ARG cc_start: 0.4521 (OUTLIER) cc_final: 0.3820 (ttp80) REVERT: B 210 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6431 (tt) REVERT: B 356 ARG cc_start: 0.7690 (pmt-80) cc_final: 0.7404 (pmt-80) REVERT: B 374 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7582 (mmmt) outliers start: 28 outliers final: 17 residues processed: 73 average time/residue: 0.5010 time to fit residues: 39.0886 Evaluate side-chains 70 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 0.0000 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100683 restraints weight = 12695.562| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.34 r_work: 0.3202 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8720 Z= 0.128 Angle : 0.546 9.621 12021 Z= 0.295 Chirality : 0.044 0.290 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.824 166.060 1436 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.90 % Favored : 95.77 % Rotamer: Outliers : 2.53 % Allowed : 23.52 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: 0.14 (0.28), residues: 923 helix: 1.74 (0.32), residues: 305 sheet: 0.09 (0.38), residues: 186 loop : -1.13 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 277 TYR 0.011 0.001 TYR A 501 PHE 0.009 0.001 PHE B 61 TRP 0.031 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 8720) covalent geometry : angle 0.54642 / 0.29 (12021) hydrogen bonds : bond 0.03714 / 2.44 ( 335) hydrogen bonds : angle 4.05805 / 2.88 ( 871) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.213 Fit side-chains REVERT: A 50 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 156 SER cc_start: 0.6865 (OUTLIER) cc_final: 0.6340 (m) REVERT: B 206 ARG cc_start: 0.4461 (OUTLIER) cc_final: 0.3814 (ttp80) REVERT: B 210 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6468 (tt) REVERT: B 356 ARG cc_start: 0.7646 (pmt-80) cc_final: 0.7374 (pmt-80) outliers start: 21 outliers final: 16 residues processed: 67 average time/residue: 0.5578 time to fit residues: 39.6835 Evaluate side-chains 69 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099269 restraints weight = 12694.372| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.32 r_work: 0.3179 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8720 Z= 0.181 Angle : 0.576 9.446 12021 Z= 0.310 Chirality : 0.045 0.311 1315 Planarity : 0.004 0.043 1372 Dihedral : 17.885 164.088 1436 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 2.53 % Allowed : 23.52 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 are not related in a simple way. whole: 0.02 (0.28), residues: 923 helix: 1.64 (0.32), residues: 304 sheet: 0.02 (0.38), residues: 186 loop : -1.19 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 277 TYR 0.011 0.001 TYR A 457 PHE 0.010 0.001 PHE A 160 TRP 0.027 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 8720) covalent geometry : angle 0.57578 / 0.31 (12021) hydrogen bonds : bond 0.04350 / 2.83 ( 335) hydrogen bonds : angle 4.14449 / 2.94 ( 871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2721.21 seconds wall clock time: 46 minutes 58.46 seconds (2818.46 seconds total)