Starting phenix.real_space_refine on Mon Jul 28 08:20:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7udb_26455/07_2025/7udb_26455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7udb_26455/07_2025/7udb_26455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7udb_26455/07_2025/7udb_26455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7udb_26455/07_2025/7udb_26455.map" model { file = "/net/cci-nas-00/data/ceres_data/7udb_26455/07_2025/7udb_26455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7udb_26455/07_2025/7udb_26455.cif" } resolution = 3.5 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4776 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4064 2.51 5 N 1114 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6472 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4424 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 27, 'TRANS': 523} Chain breaks: 3 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1675 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Time building chain proxies: 5.47, per 1000 atoms: 0.85 Number of scatterers: 6472 At special positions: 0 Unit cell: (92.88, 112.32, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1259 8.00 N 1114 7.00 C 4064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS C 36 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 65.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.789A pdb=" N CYS A 44 " --> pdb=" O MET A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.743A pdb=" N ILE A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 4.108A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Proline residue: A 95 - end of helix No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.199A pdb=" N VAL A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.927A pdb=" N SER A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.792A pdb=" N ALA A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 184 removed outlier: 3.606A pdb=" N ILE A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 removed outlier: 3.934A pdb=" N LEU A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.528A pdb=" N LEU A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 314 Processing helix chain 'A' and resid 327 through 359 Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 385 through 395 removed outlier: 3.959A pdb=" N ALA A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 415 removed outlier: 3.743A pdb=" N ILE A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.765A pdb=" N THR A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.909A pdb=" N ASP A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 4.034A pdb=" N ARG A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 removed outlier: 3.675A pdb=" N LEU A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 30 through 64 removed outlier: 3.565A pdb=" N SER B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 105 removed outlier: 3.566A pdb=" N GLU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 149 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 178 through 196 removed outlier: 3.520A pdb=" N ILE B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.994A pdb=" N ASP B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 38 through 74 removed outlier: 4.129A pdb=" N VAL C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60 removed outlier: 7.033A pdb=" N LYS A 29 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLU A 59 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 31 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 30 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU A 76 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 32 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA A 73 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 105 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 75 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA A 102 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 130 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 104 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE A 106 " --> pdb=" O GLU A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.696A pdb=" N TYR A 145 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 266 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 546 removed outlier: 6.267A pdb=" N VAL A 545 " --> pdb=" O LEU A 573 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 367 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2162 1.34 - 1.46: 1266 1.46 - 1.58: 3074 1.58 - 1.70: 0 1.70 - 1.81: 61 Bond restraints: 6563 Sorted by residual: bond pdb=" CB ASP B 140 " pdb=" CG ASP B 140 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB ASP B 27 " pdb=" CG ASP B 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CA ASP B 27 " pdb=" CB ASP B 27 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.13e-01 bond pdb=" CA THR A 455 " pdb=" CB THR A 455 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.43e-01 bond pdb=" CA VAL A 391 " pdb=" C VAL A 391 " ideal model delta sigma weight residual 1.520 1.527 -0.007 8.80e-03 1.29e+04 6.40e-01 ... (remaining 6558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 8619 1.39 - 2.78: 160 2.78 - 4.17: 39 4.17 - 5.56: 8 5.56 - 6.95: 2 Bond angle restraints: 8828 Sorted by residual: angle pdb=" N GLY B 227 " pdb=" CA GLY B 227 " pdb=" C GLY B 227 " ideal model delta sigma weight residual 110.63 115.64 -5.01 1.45e+00 4.76e-01 1.19e+01 angle pdb=" C SER A 454 " pdb=" N THR A 455 " pdb=" CA THR A 455 " ideal model delta sigma weight residual 121.54 126.05 -4.51 1.91e+00 2.74e-01 5.57e+00 angle pdb=" CB MET B 219 " pdb=" CG MET B 219 " pdb=" SD MET B 219 " ideal model delta sigma weight residual 112.70 105.75 6.95 3.00e+00 1.11e-01 5.36e+00 angle pdb=" C ARG A 275 " pdb=" N VAL A 276 " pdb=" CA VAL A 276 " ideal model delta sigma weight residual 121.97 126.12 -4.15 1.80e+00 3.09e-01 5.32e+00 angle pdb=" CA ASP B 27 " pdb=" CB ASP B 27 " pdb=" CG ASP B 27 " ideal model delta sigma weight residual 112.60 114.64 -2.04 1.00e+00 1.00e+00 4.18e+00 ... (remaining 8823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3629 17.96 - 35.92: 390 35.92 - 53.89: 85 53.89 - 71.85: 10 71.85 - 89.81: 13 Dihedral angle restraints: 4127 sinusoidal: 1738 harmonic: 2389 Sorted by residual: dihedral pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " pdb=" SG CYS C 36 " pdb=" CB CYS C 36 " ideal model delta sinusoidal sigma weight residual -86.00 -162.62 76.62 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB GLU A 12 " pdb=" CG GLU A 12 " pdb=" CD GLU A 12 " pdb=" OE1 GLU A 12 " ideal model delta sinusoidal sigma weight residual 0.00 89.81 -89.81 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA LEU A 573 " pdb=" C LEU A 573 " pdb=" N THR A 574 " pdb=" CA THR A 574 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 4124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 670 0.030 - 0.060: 215 0.060 - 0.090: 85 0.090 - 0.120: 34 0.120 - 0.150: 4 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CB VAL A 451 " pdb=" CA VAL A 451 " pdb=" CG1 VAL A 451 " pdb=" CG2 VAL A 451 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ASP B 27 " pdb=" N ASP B 27 " pdb=" C ASP B 27 " pdb=" CB ASP B 27 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1005 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 16 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C HIS A 16 " 0.044 2.00e-02 2.50e+03 pdb=" O HIS A 16 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 17 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 58 " -0.016 2.00e-02 2.50e+03 1.84e-02 5.09e+00 pdb=" CG HIS B 58 " 0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS B 58 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS B 58 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS B 58 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 58 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 94 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 95 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.032 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 257 2.73 - 3.27: 6529 3.27 - 3.81: 10336 3.81 - 4.36: 11980 4.36 - 4.90: 21091 Nonbonded interactions: 50193 Sorted by model distance: nonbonded pdb=" O ILE A 541 " pdb=" OG SER A 569 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 75 " pdb=" OD2 ASP A 90 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OD1 ASP A 210 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A 264 " pdb=" OD2 ASP A 353 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR A 358 " pdb=" OD1 ASP A 363 " model vdw 2.288 3.040 ... (remaining 50188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 74.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.380 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: 0.010 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.003 0.027 6564 Z= 0.116 Angle : 0.499 6.947 8830 Z= 0.269 Chirality : 0.038 0.150 1008 Planarity : 0.004 0.056 1132 Dihedral : 15.554 89.809 2558 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.30), residues: 787 helix: 2.32 (0.24), residues: 462 sheet: -0.28 (0.71), residues: 56 loop : -0.61 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 563 HIS 0.022 0.001 HIS B 58 PHE 0.012 0.001 PHE A 237 TYR 0.021 0.001 TYR B 141 ARG 0.006 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.12317 ( 367) hydrogen bonds : angle 4.70599 ( 1077) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.95748 ( 2) covalent geometry : bond 0.00251 ( 6563) covalent geometry : angle 0.49894 ( 8828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.354 Fit side-chains REVERT: B 30 MET cc_start: 0.6985 (mtt) cc_final: 0.6483 (mtt) REVERT: B 224 GLU cc_start: 0.7041 (tt0) cc_final: 0.6762 (mm-30) REVERT: C 71 GLN cc_start: 0.7914 (tt0) cc_final: 0.7662 (tt0) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2939 time to fit residues: 48.7468 Evaluate side-chains 98 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 0.0030 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 0.7150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 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 = 0.3946 r_free = 0.3946 target = 0.177208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133602 restraints weight = 7533.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.133663 restraints weight = 6529.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.137464 restraints weight = 5778.405| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6564 Z= 0.123 Angle : 0.501 6.938 8830 Z= 0.268 Chirality : 0.039 0.151 1008 Planarity : 0.004 0.060 1132 Dihedral : 3.485 15.718 870 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.55 % Allowed : 6.08 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.30), residues: 787 helix: 2.43 (0.24), residues: 467 sheet: -0.76 (0.65), residues: 56 loop : -0.55 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 478 HIS 0.004 0.001 HIS B 213 PHE 0.010 0.001 PHE A 310 TYR 0.012 0.001 TYR B 141 ARG 0.005 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 367) hydrogen bonds : angle 3.90590 ( 1077) SS BOND : bond 0.00343 ( 1) SS BOND : angle 0.59945 ( 2) covalent geometry : bond 0.00276 ( 6563) covalent geometry : angle 0.50110 ( 8828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.621 Fit side-chains REVERT: A 47 MET cc_start: 0.8855 (ttm) cc_final: 0.8577 (ttm) REVERT: B 138 GLN cc_start: 0.8933 (mm110) cc_final: 0.8671 (mm-40) outliers start: 4 outliers final: 0 residues processed: 112 average time/residue: 0.2487 time to fit residues: 37.8619 Evaluate side-chains 93 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 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 = 0.3953 r_free = 0.3953 target = 0.177733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133652 restraints weight = 7644.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133355 restraints weight = 5906.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.135350 restraints weight = 6329.508| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6564 Z= 0.116 Angle : 0.473 6.219 8830 Z= 0.253 Chirality : 0.039 0.150 1008 Planarity : 0.004 0.060 1132 Dihedral : 3.417 15.302 870 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.55 % Allowed : 8.84 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.30), residues: 787 helix: 2.50 (0.24), residues: 468 sheet: -0.82 (0.64), residues: 56 loop : -0.42 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 478 HIS 0.004 0.001 HIS B 58 PHE 0.008 0.001 PHE A 310 TYR 0.012 0.001 TYR B 141 ARG 0.003 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 367) hydrogen bonds : angle 3.76135 ( 1077) SS BOND : bond 0.00293 ( 1) SS BOND : angle 0.55864 ( 2) covalent geometry : bond 0.00259 ( 6563) covalent geometry : angle 0.47266 ( 8828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.829 Fit side-chains REVERT: A 47 MET cc_start: 0.8914 (ttm) cc_final: 0.8666 (ttm) REVERT: A 349 HIS cc_start: 0.8108 (m-70) cc_final: 0.7878 (m90) outliers start: 4 outliers final: 2 residues processed: 101 average time/residue: 0.2976 time to fit residues: 42.3218 Evaluate side-chains 94 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 0.0570 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 overall best weight: 0.7908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 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 = 0.3944 r_free = 0.3944 target = 0.176870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133148 restraints weight = 7646.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133508 restraints weight = 5873.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135281 restraints weight = 5991.296| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6564 Z= 0.123 Angle : 0.478 6.523 8830 Z= 0.255 Chirality : 0.039 0.145 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.395 15.131 870 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.24 % Allowed : 9.67 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.30), residues: 787 helix: 2.52 (0.24), residues: 468 sheet: -0.79 (0.64), residues: 56 loop : -0.34 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 478 HIS 0.005 0.001 HIS B 58 PHE 0.007 0.001 PHE A 310 TYR 0.013 0.001 TYR B 141 ARG 0.003 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 367) hydrogen bonds : angle 3.68568 ( 1077) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.48719 ( 2) covalent geometry : bond 0.00281 ( 6563) covalent geometry : angle 0.47800 ( 8828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.007 Fit side-chains REVERT: A 47 MET cc_start: 0.8924 (ttm) cc_final: 0.8670 (ttm) REVERT: A 349 HIS cc_start: 0.8119 (m-70) cc_final: 0.7847 (m90) REVERT: B 98 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8105 (mt0) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.2720 time to fit residues: 42.1444 Evaluate side-chains 100 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.0570 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.174417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130051 restraints weight = 7589.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129129 restraints weight = 6082.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131912 restraints weight = 6289.353| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.004 0.038 6564 Z= 0.164 Angle : 0.515 6.065 8830 Z= 0.275 Chirality : 0.041 0.149 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.497 15.837 870 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.38 % Allowed : 11.46 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.30), residues: 787 helix: 2.44 (0.24), residues: 468 sheet: -1.08 (0.60), residues: 58 loop : -0.33 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 478 HIS 0.006 0.001 HIS A 347 PHE 0.005 0.001 PHE A 310 TYR 0.014 0.001 TYR B 141 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 367) hydrogen bonds : angle 3.70292 ( 1077) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.42104 ( 2) covalent geometry : bond 0.00394 ( 6563) covalent geometry : angle 0.51467 ( 8828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.877 Fit side-chains REVERT: A 47 MET cc_start: 0.8972 (ttm) cc_final: 0.8722 (ttm) REVERT: A 398 ASN cc_start: 0.8211 (m-40) cc_final: 0.7961 (t0) REVERT: B 98 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8110 (mt0) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.1897 time to fit residues: 26.5349 Evaluate side-chains 99 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 41 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129627 restraints weight = 7492.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128816 restraints weight = 7468.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130416 restraints weight = 7186.621| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6564 Z= 0.113 Angle : 0.485 7.074 8830 Z= 0.259 Chirality : 0.039 0.143 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.418 15.064 870 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.38 % Allowed : 11.88 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.30), residues: 787 helix: 2.48 (0.24), residues: 468 sheet: -1.01 (0.60), residues: 58 loop : -0.23 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 478 HIS 0.004 0.001 HIS A 347 PHE 0.005 0.001 PHE A 310 TYR 0.011 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 367) hydrogen bonds : angle 3.64264 ( 1077) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.30610 ( 2) covalent geometry : bond 0.00252 ( 6563) covalent geometry : angle 0.48543 ( 8828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.733 Fit side-chains REVERT: A 349 HIS cc_start: 0.8105 (m-70) cc_final: 0.7860 (m90) REVERT: A 398 ASN cc_start: 0.8207 (m-40) cc_final: 0.7961 (t0) REVERT: B 98 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8063 (mt0) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.1699 time to fit residues: 23.7317 Evaluate side-chains 101 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 37 optimal weight: 0.0970 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.170963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127494 restraints weight = 7454.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128605 restraints weight = 6123.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130427 restraints weight = 5736.777| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6564 Z= 0.120 Angle : 0.490 7.003 8830 Z= 0.263 Chirality : 0.039 0.145 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.397 14.805 870 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.52 % Allowed : 12.43 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.30), residues: 787 helix: 2.52 (0.24), residues: 468 sheet: -0.83 (0.66), residues: 53 loop : -0.27 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 478 HIS 0.005 0.001 HIS B 213 PHE 0.005 0.001 PHE B 216 TYR 0.017 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 367) hydrogen bonds : angle 3.61959 ( 1077) SS BOND : bond 0.00288 ( 1) SS BOND : angle 0.55195 ( 2) covalent geometry : bond 0.00274 ( 6563) covalent geometry : angle 0.48998 ( 8828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.716 Fit side-chains REVERT: A 349 HIS cc_start: 0.8122 (m-70) cc_final: 0.7891 (m90) REVERT: B 98 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8047 (mt0) outliers start: 11 outliers final: 8 residues processed: 97 average time/residue: 0.1569 time to fit residues: 21.6176 Evaluate side-chains 100 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.0050 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.176450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133241 restraints weight = 7540.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.133343 restraints weight = 5655.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.136067 restraints weight = 5090.896| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6564 Z= 0.115 Angle : 0.490 7.031 8830 Z= 0.264 Chirality : 0.039 0.143 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.351 14.440 870 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.38 % Allowed : 12.15 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.30), residues: 787 helix: 2.54 (0.24), residues: 468 sheet: -0.77 (0.66), residues: 53 loop : -0.18 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 478 HIS 0.004 0.001 HIS B 213 PHE 0.010 0.001 PHE A 310 TYR 0.019 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 367) hydrogen bonds : angle 3.59210 ( 1077) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.33478 ( 2) covalent geometry : bond 0.00257 ( 6563) covalent geometry : angle 0.49042 ( 8828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.765 Fit side-chains REVERT: A 47 MET cc_start: 0.8935 (ttm) cc_final: 0.8683 (ttm) REVERT: A 349 HIS cc_start: 0.8130 (m-70) cc_final: 0.7887 (m90) REVERT: B 98 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: C 38 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7092 (tm-30) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.1677 time to fit residues: 23.4271 Evaluate side-chains 99 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 0.0050 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.172998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132119 restraints weight = 7618.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131061 restraints weight = 6924.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133101 restraints weight = 7509.493| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6564 Z= 0.109 Angle : 0.507 9.133 8830 Z= 0.272 Chirality : 0.039 0.143 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.324 13.986 870 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.24 % Allowed : 12.71 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.30), residues: 787 helix: 2.56 (0.24), residues: 468 sheet: -0.69 (0.66), residues: 53 loop : -0.14 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 563 HIS 0.005 0.001 HIS B 213 PHE 0.004 0.001 PHE A 137 TYR 0.021 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 367) hydrogen bonds : angle 3.58521 ( 1077) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.20311 ( 2) covalent geometry : bond 0.00237 ( 6563) covalent geometry : angle 0.50686 ( 8828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.700 Fit side-chains REVERT: A 349 HIS cc_start: 0.8105 (m-70) cc_final: 0.7879 (m90) REVERT: B 98 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8066 (mt0) outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.1594 time to fit residues: 23.1677 Evaluate side-chains 100 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.169856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128316 restraints weight = 7635.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126798 restraints weight = 7016.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129049 restraints weight = 7397.975| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6564 Z= 0.149 Angle : 0.537 8.237 8830 Z= 0.287 Chirality : 0.040 0.166 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.441 14.830 870 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.24 % Allowed : 13.26 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.30), residues: 787 helix: 2.51 (0.24), residues: 468 sheet: -0.73 (0.66), residues: 53 loop : -0.19 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 478 HIS 0.005 0.001 HIS A 347 PHE 0.005 0.001 PHE A 540 TYR 0.023 0.001 TYR B 141 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 367) hydrogen bonds : angle 3.62293 ( 1077) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.10683 ( 2) covalent geometry : bond 0.00354 ( 6563) covalent geometry : angle 0.53733 ( 8828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.792 Fit side-chains REVERT: A 349 HIS cc_start: 0.8138 (m-70) cc_final: 0.7905 (m90) REVERT: B 98 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8076 (mt0) outliers start: 9 outliers final: 8 residues processed: 97 average time/residue: 0.1522 time to fit residues: 21.1098 Evaluate side-chains 99 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 0.0670 chunk 41 optimal weight: 0.0980 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 30.0000 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.171896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131003 restraints weight = 7689.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130031 restraints weight = 6858.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131690 restraints weight = 7747.673| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6564 Z= 0.115 Angle : 0.514 8.028 8830 Z= 0.276 Chirality : 0.039 0.164 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.369 14.269 870 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.10 % Allowed : 13.67 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.30), residues: 787 helix: 2.56 (0.24), residues: 468 sheet: -0.63 (0.66), residues: 53 loop : -0.17 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 478 HIS 0.004 0.001 HIS A 347 PHE 0.004 0.001 PHE B 216 TYR 0.021 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 367) hydrogen bonds : angle 3.59737 ( 1077) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.17719 ( 2) covalent geometry : bond 0.00254 ( 6563) covalent geometry : angle 0.51397 ( 8828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.19 seconds wall clock time: 49 minutes 48.15 seconds (2988.15 seconds total)