Starting phenix.real_space_refine on Thu Mar 13 00:17:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vbe_43122/03_2025/8vbe_43122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vbe_43122/03_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_43122/03_2025/8vbe_43122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vbe_43122/03_2025/8vbe_43122.map" model { file = "/net/cci-nas-00/data/ceres_data/8vbe_43122/03_2025/8vbe_43122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vbe_43122/03_2025/8vbe_43122.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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: 5.87, per 1000 atoms: 0.70 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: 2.12 Conformation dependent library (CDL) restraints added in 809.9 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: 2.67 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: 2.41 Time building geometry restraints manager: 2.47 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: 3.720 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.710 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- 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= 0.235 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (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 TRP 0.012 0.001 TRP B 410 HIS 0.003 0.001 HIS B 198 PHE 0.008 0.001 PHE B 61 TYR 0.010 0.001 TYR A 501 ARG 0.015 0.001 ARG B 277 *********************** 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 : 0.863 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: 1.2306 time to fit residues: 113.1173 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 : 0.969 ------------------------------------------------------------------------------- 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 80 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.126781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099275 restraints weight = 12599.446| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.33 r_work: 0.3177 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0772 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= 0.296 Angle : 0.587 6.932 12021 Z= 0.316 Chirality : 0.044 0.168 1315 Planarity : 0.005 0.041 1372 Dihedral : 18.535 153.440 1475 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.55 % Favored : 95.02 % Rotamer: Outliers : 5.07 % Allowed : 19.78 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.28), residues: 923 helix: 1.10 (0.31), residues: 311 sheet: -0.08 (0.37), residues: 186 loop : -1.36 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 88 HIS 0.005 0.001 HIS A 198 PHE 0.010 0.001 PHE B 61 TYR 0.012 0.001 TYR A 457 ARG 0.007 0.001 ARG A 358 *********************** 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 97 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 0.848 Fit side-chains REVERT: A 50 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8086 (mp) REVERT: A 413 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: A 500 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: B 374 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7630 (mmmt) outliers start: 42 outliers final: 24 residues processed: 93 average time/residue: 1.3417 time to fit residues: 132.4037 Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 12 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 296 THR Chi-restraints excluded: chain B residue 315 HIS 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 22 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.126032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098566 restraints weight = 12688.574| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.34 r_work: 0.3164 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8720 Z= 0.315 Angle : 0.585 6.904 12021 Z= 0.313 Chirality : 0.044 0.163 1315 Planarity : 0.005 0.042 1372 Dihedral : 18.098 160.186 1453 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.55 % Favored : 95.02 % Rotamer: Outliers : 5.19 % Allowed : 20.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.27), residues: 923 helix: 1.12 (0.31), residues: 311 sheet: -0.16 (0.37), residues: 186 loop : -1.41 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 88 HIS 0.005 0.001 HIS A 198 PHE 0.010 0.001 PHE B 61 TYR 0.012 0.001 TYR A 144 ARG 0.006 0.001 ARG A 358 *********************** 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 96 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 53 time to evaluate : 0.854 Fit side-chains REVERT: A 50 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 413 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: B 277 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6988 (ttp80) REVERT: B 281 LYS cc_start: 0.7241 (ttmt) cc_final: 0.7031 (ttmt) REVERT: B 356 ARG cc_start: 0.7575 (pmt-80) cc_final: 0.7293 (pmt-80) REVERT: B 374 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7608 (mmmt) outliers start: 43 outliers final: 22 residues processed: 89 average time/residue: 1.3724 time to fit residues: 129.6739 Evaluate side-chains 75 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 189 VAL Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 317 VAL 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 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.125848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098443 restraints weight = 12648.286| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.34 r_work: 0.3163 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8720 Z= 0.301 Angle : 0.570 6.865 12021 Z= 0.306 Chirality : 0.044 0.155 1315 Planarity : 0.005 0.042 1372 Dihedral : 17.797 162.593 1444 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.98 % Favored : 94.58 % Rotamer: Outliers : 5.67 % Allowed : 19.66 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 923 helix: 1.36 (0.32), residues: 303 sheet: -0.15 (0.37), residues: 186 loop : -1.41 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 406 HIS 0.005 0.001 HIS B 198 PHE 0.011 0.001 PHE B 61 TYR 0.011 0.001 TYR A 144 ARG 0.007 0.001 ARG B 284 *********************** 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: 47 poor density : 54 time to evaluate : 0.853 Fit side-chains REVERT: A 50 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 413 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: B 206 ARG cc_start: 0.4535 (OUTLIER) cc_final: 0.3874 (ttp80) REVERT: B 210 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6451 (tt) REVERT: B 278 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: B 374 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7613 (mmmt) outliers start: 47 outliers final: 22 residues processed: 92 average time/residue: 1.2190 time to fit residues: 119.5788 Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 413 GLU 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 117 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 275 LYS 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 362 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 68 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 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 = 0.3705 r_free = 0.3705 target = 0.128024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100680 restraints weight = 12580.718| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.33 r_work: 0.3200 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1186 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= 0.182 Angle : 0.518 7.016 12021 Z= 0.278 Chirality : 0.041 0.148 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.538 167.904 1440 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.01 % Favored : 95.67 % Rotamer: Outliers : 4.95 % Allowed : 20.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.28), residues: 923 helix: 1.50 (0.32), residues: 311 sheet: 0.01 (0.37), residues: 186 loop : -1.29 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 PHE 0.009 0.001 PHE B 61 TYR 0.011 0.001 TYR A 501 ARG 0.008 0.001 ARG B 277 *********************** 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 99 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 58 time to evaluate : 0.925 Fit side-chains REVERT: A 50 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8086 (mp) REVERT: B 72 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8074 (ttt180) REVERT: B 206 ARG cc_start: 0.4445 (OUTLIER) cc_final: 0.3822 (ttp80) REVERT: B 210 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6457 (tt) REVERT: B 277 ARG cc_start: 0.7349 (ttp80) cc_final: 0.7089 (ttp80) REVERT: B 278 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: B 297 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6147 (mm-30) outliers start: 41 outliers final: 18 residues processed: 90 average time/residue: 1.3213 time to fit residues: 126.7486 Evaluate side-chains 76 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 58 THR 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 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 192 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 275 LYS 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 386 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 52 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097868 restraints weight = 12685.848| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.34 r_work: 0.3155 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 8720 Z= 0.347 Angle : 0.588 7.295 12021 Z= 0.314 Chirality : 0.044 0.159 1315 Planarity : 0.005 0.043 1372 Dihedral : 17.705 162.595 1437 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.31 % Favored : 94.37 % Rotamer: Outliers : 5.43 % Allowed : 20.39 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 923 helix: 1.14 (0.31), residues: 316 sheet: -0.14 (0.37), residues: 186 loop : -1.41 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 406 HIS 0.005 0.001 HIS A 198 PHE 0.011 0.001 PHE B 61 TYR 0.013 0.002 TYR A 457 ARG 0.006 0.001 ARG B 284 *********************** 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 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 49 time to evaluate : 1.085 Fit side-chains REVERT: A 50 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8051 (mp) REVERT: B 156 SER cc_start: 0.6916 (OUTLIER) cc_final: 0.6292 (m) REVERT: B 206 ARG cc_start: 0.4507 (OUTLIER) cc_final: 0.3820 (ttp80) REVERT: B 210 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6460 (tt) REVERT: B 278 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: B 297 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6220 (mm-30) REVERT: B 374 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7598 (mmmt) outliers start: 45 outliers final: 22 residues processed: 87 average time/residue: 1.4595 time to fit residues: 134.7930 Evaluate side-chains 76 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 245 VAL Chi-restraints excluded: chain B residue 275 LYS 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 305 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 Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100177 restraints weight = 12697.510| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.34 r_work: 0.3191 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1317 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= 0.202 Angle : 0.531 7.388 12021 Z= 0.284 Chirality : 0.042 0.149 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.522 166.958 1437 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.23 % Favored : 95.45 % Rotamer: Outliers : 4.22 % Allowed : 21.59 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 923 helix: 1.48 (0.32), residues: 310 sheet: 0.00 (0.38), residues: 186 loop : -1.29 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 PHE 0.010 0.001 PHE B 61 TYR 0.011 0.001 TYR A 501 ARG 0.010 0.001 ARG B 277 *********************** 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 85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 50 time to evaluate : 0.960 Fit side-chains REVERT: A 50 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 156 SER cc_start: 0.6842 (OUTLIER) cc_final: 0.6292 (m) REVERT: B 206 ARG cc_start: 0.4481 (OUTLIER) cc_final: 0.3807 (ttp80) REVERT: B 210 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6441 (tt) REVERT: B 277 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7166 (ttp80) REVERT: B 278 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: B 297 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6155 (mm-30) outliers start: 35 outliers final: 19 residues processed: 80 average time/residue: 1.4327 time to fit residues: 122.0669 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 : 0.869 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 1 optimal weight: 0.0070 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.127689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100325 restraints weight = 12741.801| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.35 r_work: 0.3193 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1383 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= 0.202 Angle : 0.527 7.413 12021 Z= 0.281 Chirality : 0.042 0.156 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.423 167.838 1437 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.33 % Favored : 95.34 % Rotamer: Outliers : 3.86 % Allowed : 21.95 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 923 helix: 1.50 (0.32), residues: 311 sheet: 0.03 (0.38), residues: 186 loop : -1.25 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 PHE 0.010 0.001 PHE B 61 TYR 0.011 0.001 TYR A 501 ARG 0.009 0.001 ARG B 277 *********************** 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: 32 poor density : 52 time to evaluate : 0.839 Fit side-chains REVERT: A 50 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 72 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8067 (ttt180) REVERT: B 123 ASP cc_start: 0.8527 (t0) cc_final: 0.8177 (m-30) REVERT: B 156 SER cc_start: 0.6894 (OUTLIER) cc_final: 0.6364 (m) REVERT: B 206 ARG cc_start: 0.4452 (OUTLIER) cc_final: 0.3792 (ttp80) REVERT: B 210 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6382 (tt) REVERT: B 277 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7250 (ttp80) REVERT: B 278 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7292 (tt0) outliers start: 32 outliers final: 19 residues processed: 79 average time/residue: 1.2593 time to fit residues: 106.4615 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 : 0.848 ------------------------------------------------------------------------------- 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 58 THR 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 B residue 72 ARG 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 386 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 0.9980 chunk 22 optimal weight: 0.0030 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN A 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101339 restraints weight = 12814.308| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.36 r_work: 0.3211 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1429 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= 0.165 Angle : 0.514 7.448 12021 Z= 0.274 Chirality : 0.041 0.151 1315 Planarity : 0.004 0.042 1372 Dihedral : 17.324 169.847 1437 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.79 % Favored : 95.88 % Rotamer: Outliers : 2.90 % Allowed : 22.92 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.28), residues: 923 helix: 1.60 (0.32), residues: 311 sheet: 0.08 (0.38), residues: 186 loop : -1.16 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 406 HIS 0.004 0.001 HIS B 198 PHE 0.010 0.001 PHE B 61 TYR 0.011 0.001 TYR A 501 ARG 0.008 0.001 ARG B 277 *********************** 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: 24 poor density : 53 time to evaluate : 0.966 Fit side-chains REVERT: A 50 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 53 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6600 (pp20) REVERT: B 123 ASP cc_start: 0.8534 (t0) cc_final: 0.8228 (m-30) REVERT: B 156 SER cc_start: 0.6833 (OUTLIER) cc_final: 0.6335 (m) REVERT: B 206 ARG cc_start: 0.4411 (OUTLIER) cc_final: 0.3761 (ttp80) REVERT: B 210 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6377 (tt) REVERT: B 278 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: B 308 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7525 (tm-30) outliers start: 24 outliers final: 15 residues processed: 74 average time/residue: 1.6512 time to fit residues: 129.9763 Evaluate side-chains 72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 362 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 475 GLN 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 380 ILE Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5289 > 50: distance: 4 - 9: 8.482 distance: 9 - 10: 9.936 distance: 10 - 11: 10.135 distance: 10 - 13: 3.956 distance: 11 - 12: 12.284 distance: 11 - 17: 10.757 distance: 13 - 14: 12.874 distance: 13 - 15: 14.408 distance: 14 - 16: 26.767 distance: 17 - 18: 30.073 distance: 18 - 19: 17.492 distance: 18 - 21: 16.049 distance: 19 - 20: 29.688 distance: 19 - 24: 9.147 distance: 21 - 22: 6.961 distance: 21 - 23: 33.850 distance: 24 - 25: 9.812 distance: 25 - 26: 28.036 distance: 25 - 28: 42.486 distance: 26 - 27: 3.779 distance: 26 - 32: 29.398 distance: 28 - 29: 21.209 distance: 29 - 30: 17.097 distance: 29 - 31: 45.736 distance: 32 - 33: 5.759 distance: 32 - 38: 19.238 distance: 33 - 34: 8.774 distance: 33 - 36: 20.039 distance: 34 - 35: 29.712 distance: 34 - 39: 7.895 distance: 36 - 37: 16.166 distance: 37 - 38: 23.419 distance: 39 - 40: 27.054 distance: 40 - 41: 17.219 distance: 40 - 43: 15.494 distance: 41 - 42: 8.298 distance: 41 - 48: 15.143 distance: 43 - 44: 27.874 distance: 44 - 45: 23.646 distance: 45 - 46: 10.471 distance: 45 - 47: 4.727 distance: 48 - 49: 13.400 distance: 49 - 50: 15.279 distance: 49 - 52: 24.161 distance: 50 - 51: 18.745 distance: 50 - 57: 16.305 distance: 52 - 53: 25.550 distance: 53 - 54: 21.177 distance: 54 - 55: 37.059 distance: 55 - 56: 37.602 distance: 57 - 58: 27.738 distance: 58 - 59: 10.170 distance: 58 - 61: 23.299 distance: 59 - 60: 9.421 distance: 59 - 65: 18.442 distance: 61 - 62: 14.901 distance: 62 - 63: 23.645 distance: 62 - 64: 28.831 distance: 65 - 66: 9.423 distance: 66 - 67: 15.664 distance: 66 - 69: 41.414 distance: 67 - 68: 32.401 distance: 67 - 71: 9.168 distance: 69 - 70: 20.649 distance: 71 - 72: 12.929 distance: 72 - 73: 25.301 distance: 72 - 75: 27.996 distance: 73 - 74: 19.373 distance: 73 - 85: 27.563 distance: 75 - 76: 9.791 distance: 76 - 77: 17.643 distance: 76 - 78: 17.124 distance: 77 - 79: 9.701 distance: 78 - 80: 20.896 distance: 78 - 81: 14.488 distance: 79 - 80: 14.672 distance: 80 - 82: 21.521 distance: 81 - 83: 24.183 distance: 82 - 84: 9.356 distance: 83 - 84: 7.281 distance: 85 - 86: 14.303 distance: 86 - 87: 13.054 distance: 86 - 89: 9.960 distance: 87 - 88: 15.040 distance: 87 - 92: 12.930 distance: 88 - 114: 29.667 distance: 89 - 90: 31.136 distance: 89 - 91: 11.585