Starting phenix.real_space_refine on Wed Sep 17 11:38:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vbe_43122/09_2025/8vbe_43122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vbe_43122/09_2025/8vbe_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_43122/09_2025/8vbe_43122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vbe_43122/09_2025/8vbe_43122.map" model { file = "/net/cci-nas-00/data/ceres_data/8vbe_43122/09_2025/8vbe_43122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vbe_43122/09_2025/8vbe_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): 0.01s 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: 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: 2.14, per 1000 atoms: 0.25 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: 0.75 Conformation dependent library (CDL) restraints added in 276.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.11 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: 1.29 Time building geometry restraints manager: 0.99 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 - 1.89: 11698 1.89 - 3.78: 273 3.78 - 5.67: 41 5.67 - 7.56: 6 7.56 - 9.45: 3 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=" O3' DG F 19 " pdb=" C3' DG F 19 " pdb=" C2' DG F 19 " ideal model delta sigma weight residual 111.50 102.05 9.45 1.50e+00 4.44e-01 3.97e+01 angle pdb=" O3' DG F 14 " pdb=" C3' DG F 14 " pdb=" C2' DG F 14 " ideal model delta sigma weight residual 111.50 103.51 7.99 1.50e+00 4.44e-01 2.84e+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 ... (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: 1055 0.053 - 0.106: 212 0.106 - 0.158: 43 0.158 - 0.211: 3 0.211 - 0.264: 2 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=" C3' DG F 19 " pdb=" C4' DG F 19 " pdb=" O3' DG F 19 " pdb=" C2' DG F 19 " both_signs ideal model delta sigma weight residual False -2.66 -2.91 0.25 2.00e-01 2.50e+01 1.52e+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 ... (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: 3.980 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.010 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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= 0.218 Angle : 0.682 9.451 12021 Z= 0.415 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00383 ( 8720) covalent geometry : angle 0.68235 (12021) hydrogen bonds : bond 0.17766 ( 335) hydrogen bonds : angle 5.58432 ( 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 : 0.192 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: 0.5698 time to fit residues: 51.9668 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 : 0.356 ------------------------------------------------------------------------------- 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 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3668 r_free = 0.3668 target = 0.125087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097614 restraints weight = 12738.021| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.34 r_work: 0.3150 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 8720 Z= 0.269 Angle : 0.639 7.070 12021 Z= 0.343 Chirality : 0.046 0.166 1315 Planarity : 0.005 0.042 1372 Dihedral : 18.708 153.158 1475 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.66 % Favored : 94.80 % Rotamer: Outliers : 5.19 % Allowed : 19.78 % Favored : 75.03 % 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 aren not related in a simple way. whole: -0.63 (0.27), residues: 923 helix: 0.76 (0.31), residues: 317 sheet: -0.21 (0.37), residues: 186 loop : -1.42 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 358 TYR 0.015 0.002 TYR A 457 PHE 0.011 0.002 PHE A 160 TRP 0.013 0.002 TRP A 88 HIS 0.006 0.002 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 8720) covalent geometry : angle 0.63876 (12021) hydrogen bonds : bond 0.05844 ( 335) hydrogen bonds : angle 4.59395 ( 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 96 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 53 time to evaluate : 0.325 Fit side-chains REVERT: A 50 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8033 (mp) REVERT: A 413 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: B 275 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6254 (mtmm) REVERT: B 374 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7619 (mmmt) outliers start: 43 outliers final: 24 residues processed: 91 average time/residue: 0.6288 time to fit residues: 60.6133 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 : 0.251 ------------------------------------------------------------------------------- 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 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 189 VAL Chi-restraints excluded: chain B residue 191 SER 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: 0.5980 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 367 GLN A 373 GLN B 394 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100489 restraints weight = 12563.510| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.33 r_work: 0.3196 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8720 Z= 0.139 Angle : 0.535 6.887 12021 Z= 0.287 Chirality : 0.042 0.163 1315 Planarity : 0.004 0.041 1372 Dihedral : 17.947 163.880 1453 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.90 % Favored : 95.67 % Rotamer: Outliers : 5.19 % Allowed : 20.02 % 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 aren not related in a simple way. whole: -0.30 (0.28), residues: 923 helix: 1.26 (0.32), residues: 311 sheet: -0.08 (0.37), residues: 186 loop : -1.37 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 358 TYR 0.011 0.001 TYR A 501 PHE 0.009 0.001 PHE B 61 TRP 0.012 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8720) covalent geometry : angle 0.53497 (12021) hydrogen bonds : bond 0.04055 ( 335) hydrogen bonds : angle 4.22553 ( 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: 43 poor density : 52 time to evaluate : 0.324 Fit side-chains REVERT: A 50 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 277 ARG cc_start: 0.7419 (ttp80) cc_final: 0.7188 (ttp80) REVERT: B 356 ARG cc_start: 0.7589 (pmt-80) cc_final: 0.7339 (pmt-80) outliers start: 43 outliers final: 20 residues processed: 89 average time/residue: 0.6120 time to fit residues: 57.7750 Evaluate side-chains 71 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 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 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 536 VAL Chi-restraints excluded: chain B residue 68 SER 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 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 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.128467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100944 restraints weight = 12773.387| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.36 r_work: 0.3205 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8720 Z= 0.128 Angle : 0.515 6.947 12021 Z= 0.276 Chirality : 0.041 0.159 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.518 169.096 1443 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.33 % Favored : 95.23 % Rotamer: Outliers : 4.58 % Allowed : 20.87 % 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 aren not related in a simple way. whole: -0.04 (0.28), residues: 923 helix: 1.60 (0.32), residues: 305 sheet: 0.02 (0.37), residues: 186 loop : -1.26 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 358 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 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8720) covalent geometry : angle 0.51506 (12021) hydrogen bonds : bond 0.03672 ( 335) hydrogen bonds : angle 4.04877 ( 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 100 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.315 Fit side-chains REVERT: A 50 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8075 (mp) REVERT: B 123 ASP cc_start: 0.8561 (t70) cc_final: 0.8171 (m-30) REVERT: B 206 ARG cc_start: 0.4442 (OUTLIER) cc_final: 0.3842 (ttp80) REVERT: B 278 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: B 356 ARG cc_start: 0.7572 (pmt-80) cc_final: 0.7327 (pmt-80) outliers start: 38 outliers final: 14 residues processed: 93 average time/residue: 0.5679 time to fit residues: 56.1052 Evaluate side-chains 72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 B residue 68 SER Chi-restraints excluded: chain B residue 102 LYS 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 278 GLN 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 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: 0.5980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098493 restraints weight = 12816.971| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.34 r_work: 0.3165 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 8720 Z= 0.202 Angle : 0.566 6.931 12021 Z= 0.303 Chirality : 0.044 0.157 1315 Planarity : 0.005 0.042 1372 Dihedral : 17.646 163.990 1438 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.77 % Favored : 94.91 % Rotamer: Outliers : 5.43 % Allowed : 20.63 % 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 aren not related in a simple way. whole: -0.21 (0.27), residues: 923 helix: 1.45 (0.31), residues: 304 sheet: -0.08 (0.37), residues: 186 loop : -1.35 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 277 TYR 0.013 0.001 TYR A 457 PHE 0.010 0.001 PHE A 160 TRP 0.011 0.001 TRP A 402 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 8720) covalent geometry : angle 0.56594 (12021) hydrogen bonds : bond 0.04635 ( 335) hydrogen bonds : angle 4.22646 ( 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 97 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 52 time to evaluate : 0.356 Fit side-chains REVERT: A 50 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 72 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8075 (ttt180) REVERT: B 123 ASP cc_start: 0.8551 (t70) cc_final: 0.8205 (m-30) REVERT: B 206 ARG cc_start: 0.4538 (OUTLIER) cc_final: 0.3863 (ttp80) REVERT: B 277 ARG cc_start: 0.7550 (ttp80) cc_final: 0.7303 (ttp80) REVERT: B 278 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: B 297 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6207 (mm-30) REVERT: B 356 ARG cc_start: 0.7630 (pmt-80) cc_final: 0.7360 (pmt-80) REVERT: B 374 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7579 (mmmt) outliers start: 45 outliers final: 22 residues processed: 91 average time/residue: 0.6184 time to fit residues: 59.6177 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 : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ILE 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 301 LEU 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 536 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 72 ARG 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 192 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 278 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101279 restraints weight = 12610.362| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.34 r_work: 0.3210 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8720 Z= 0.118 Angle : 0.509 7.458 12021 Z= 0.272 Chirality : 0.041 0.146 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.396 169.529 1437 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.23 % Favored : 95.45 % 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 aren not related in a simple way. whole: 0.08 (0.28), residues: 923 helix: 1.71 (0.32), residues: 305 sheet: 0.07 (0.38), residues: 186 loop : -1.19 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 277 TYR 0.011 0.001 TYR A 501 PHE 0.008 0.001 PHE B 61 TRP 0.018 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8720) covalent geometry : angle 0.50865 (12021) hydrogen bonds : bond 0.03419 ( 335) hydrogen bonds : angle 3.99128 ( 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 89 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.258 Fit side-chains REVERT: A 50 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 53 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6587 (pp20) REVERT: B 72 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8101 (ttt180) REVERT: B 123 ASP cc_start: 0.8496 (t70) cc_final: 0.8226 (m-30) REVERT: B 206 ARG cc_start: 0.4415 (OUTLIER) cc_final: 0.3789 (ttp80) REVERT: B 210 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6467 (tt) REVERT: B 278 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: B 297 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6165 (mm-30) REVERT: B 356 ARG cc_start: 0.7545 (pmt-80) cc_final: 0.7295 (pmt-80) outliers start: 32 outliers final: 17 residues processed: 82 average time/residue: 0.6453 time to fit residues: 56.0358 Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 301 LEU 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 500 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 72 ARG Chi-restraints excluded: chain B residue 102 LYS 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 278 GLN 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 386 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099514 restraints weight = 12879.704| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.37 r_work: 0.3182 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8720 Z= 0.165 Angle : 0.545 7.409 12021 Z= 0.290 Chirality : 0.042 0.154 1315 Planarity : 0.004 0.043 1372 Dihedral : 17.470 166.646 1437 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 4.95 % Allowed : 21.35 % Favored : 73.70 % 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 aren not related in a simple way. whole: -0.01 (0.28), residues: 923 helix: 1.61 (0.32), residues: 305 sheet: 0.01 (0.38), residues: 186 loop : -1.22 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 277 TYR 0.011 0.001 TYR A 144 PHE 0.010 0.001 PHE B 61 TRP 0.023 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8720) covalent geometry : angle 0.54460 (12021) hydrogen bonds : bond 0.04102 ( 335) hydrogen bonds : angle 4.08782 ( 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 92 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 51 time to evaluate : 0.326 Fit side-chains REVERT: A 50 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 123 ASP cc_start: 0.8504 (t70) cc_final: 0.8223 (m-30) REVERT: B 156 SER cc_start: 0.6892 (OUTLIER) cc_final: 0.6349 (m) REVERT: B 206 ARG cc_start: 0.4527 (OUTLIER) cc_final: 0.3830 (ttp80) REVERT: B 210 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6490 (tt) REVERT: B 277 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7162 (ttp80) REVERT: B 278 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: B 356 ARG cc_start: 0.7613 (pmt-80) cc_final: 0.7351 (pmt-80) REVERT: B 374 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7584 (mmmt) outliers start: 41 outliers final: 19 residues processed: 86 average time/residue: 0.6584 time to fit residues: 59.6887 Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 301 LEU 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 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 278 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099411 restraints weight = 12652.752| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.34 r_work: 0.3180 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.004 0.024 8720 Z= 0.167 Angle : 0.548 7.360 12021 Z= 0.292 Chirality : 0.043 0.156 1315 Planarity : 0.004 0.043 1372 Dihedral : 17.491 165.396 1437 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.77 % Favored : 94.91 % Rotamer: Outliers : 4.10 % Allowed : 22.07 % 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 aren not related in a simple way. whole: -0.02 (0.28), residues: 923 helix: 1.61 (0.32), residues: 304 sheet: 0.00 (0.38), residues: 186 loop : -1.23 (0.28), residues: 433 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 0.009 0.001 PHE A 160 TRP 0.029 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8720) covalent geometry : angle 0.54763 (12021) hydrogen bonds : bond 0.04135 ( 335) hydrogen bonds : angle 4.11815 ( 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 84 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 50 time to evaluate : 0.319 Fit side-chains REVERT: A 50 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 123 ASP cc_start: 0.8494 (t70) cc_final: 0.8225 (m-30) REVERT: B 206 ARG cc_start: 0.4510 (OUTLIER) cc_final: 0.3808 (ttp80) REVERT: B 210 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6465 (tt) REVERT: B 277 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7296 (ttp80) REVERT: B 278 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 356 ARG cc_start: 0.7620 (pmt-80) cc_final: 0.7361 (pmt-80) REVERT: B 374 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7575 (mmmt) outliers start: 34 outliers final: 20 residues processed: 79 average time/residue: 0.6771 time to fit residues: 56.5143 Evaluate side-chains 73 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 301 LEU 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 68 SER Chi-restraints excluded: chain B residue 102 LYS 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 278 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099980 restraints weight = 12654.888| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.36 r_work: 0.3181 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8720 Z= 0.132 Angle : 0.522 7.433 12021 Z= 0.277 Chirality : 0.042 0.154 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.385 167.957 1437 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.55 % Favored : 95.12 % Rotamer: Outliers : 3.62 % Allowed : 22.56 % 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 aren not related in a simple way. whole: 0.11 (0.28), residues: 923 helix: 1.70 (0.32), residues: 305 sheet: 0.08 (0.38), residues: 186 loop : -1.15 (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 0.009 0.001 PHE B 61 TRP 0.038 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8720) covalent geometry : angle 0.52168 (12021) hydrogen bonds : bond 0.03618 ( 335) hydrogen bonds : angle 4.00855 ( 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 83 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.233 Fit side-chains REVERT: A 50 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 53 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6562 (pp20) REVERT: A 404 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8777 (mt-10) REVERT: B 123 ASP cc_start: 0.8409 (t70) cc_final: 0.8096 (m-30) REVERT: B 156 SER cc_start: 0.6625 (OUTLIER) cc_final: 0.6091 (m) REVERT: B 206 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.3617 (ttp80) REVERT: B 374 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7250 (mmmt) outliers start: 30 outliers final: 18 residues processed: 79 average time/residue: 0.6199 time to fit residues: 51.8790 Evaluate side-chains 73 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 301 LEU 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 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 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 Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 0.0040 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3701 r_free = 0.3701 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100245 restraints weight = 12635.395| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.40 r_work: 0.3187 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8720 Z= 0.126 Angle : 0.534 7.449 12021 Z= 0.283 Chirality : 0.041 0.152 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.261 169.280 1437 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.33 % Favored : 95.34 % Rotamer: Outliers : 3.02 % Allowed : 23.40 % Favored : 73.58 % 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 aren not related in a simple way. whole: 0.15 (0.28), residues: 923 helix: 1.76 (0.32), residues: 306 sheet: 0.09 (0.38), residues: 186 loop : -1.13 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 277 TYR 0.011 0.001 TYR A 501 PHE 0.010 0.001 PHE B 61 TRP 0.046 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8720) covalent geometry : angle 0.53354 (12021) hydrogen bonds : bond 0.03475 ( 335) hydrogen bonds : angle 3.93362 ( 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 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.355 Fit side-chains REVERT: A 50 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7986 (mp) REVERT: A 404 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8763 (mt-10) REVERT: B 123 ASP cc_start: 0.8398 (t70) cc_final: 0.8155 (m-30) REVERT: B 156 SER cc_start: 0.6668 (OUTLIER) cc_final: 0.6124 (m) REVERT: B 206 ARG cc_start: 0.4188 (OUTLIER) cc_final: 0.3601 (ttp80) REVERT: B 277 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7146 (ttp80) REVERT: B 308 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7435 (tm-30) REVERT: B 374 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7260 (mmmt) outliers start: 25 outliers final: 17 residues processed: 76 average time/residue: 0.6251 time to fit residues: 50.5153 Evaluate side-chains 71 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 301 LEU 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 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 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 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3698 r_free = 0.3698 target = 0.128045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100124 restraints weight = 12600.409| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.40 r_work: 0.3183 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8720 Z= 0.134 Angle : 0.534 7.443 12021 Z= 0.283 Chirality : 0.041 0.154 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.119 168.595 1433 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.77 % Allowed : 23.40 % 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 aren not related in a simple way. whole: 0.13 (0.28), residues: 923 helix: 1.74 (0.32), residues: 306 sheet: 0.06 (0.38), residues: 186 loop : -1.15 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 277 TYR 0.011 0.001 TYR A 501 PHE 0.009 0.001 PHE B 61 TRP 0.051 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8720) covalent geometry : angle 0.53437 (12021) hydrogen bonds : bond 0.03582 ( 335) hydrogen bonds : angle 3.94898 ( 871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3224.68 seconds wall clock time: 55 minutes 41.89 seconds (3341.89 seconds total)