Starting phenix.real_space_refine on Wed Mar 4 02:30:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7udb_26455/03_2026/7udb_26455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7udb_26455/03_2026/7udb_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_26455/03_2026/7udb_26455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7udb_26455/03_2026/7udb_26455.map" model { file = "/net/cci-nas-00/data/ceres_data/7udb_26455/03_2026/7udb_26455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7udb_26455/03_2026/7udb_26455.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.58, per 1000 atoms: 0.24 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: 0.75 Conformation dependent library (CDL) restraints added in 214.4 milliseconds 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: 0.17 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: 0.97 Time building geometry restraints manager: 0.94 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.420 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.210 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.006 0.000 ARG A 39 TYR 0.021 0.001 TYR B 141 PHE 0.012 0.001 PHE A 237 TRP 0.002 0.000 TRP A 563 HIS 0.022 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6563) covalent geometry : angle 0.49894 ( 8828) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.95748 ( 2) hydrogen bonds : bond 0.12317 ( 367) hydrogen bonds : angle 4.70599 ( 1077) *********************** 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 : 0.240 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: 0.7913 (tt0) cc_final: 0.7662 (tt0) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.0756 time to fit residues: 12.4140 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 : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.172412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129024 restraints weight = 7660.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126898 restraints weight = 6163.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130713 restraints weight = 5918.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130978 restraints weight = 3859.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131933 restraints weight = 3866.856| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6564 Z= 0.217 Angle : 0.569 7.306 8830 Z= 0.301 Chirality : 0.042 0.154 1008 Planarity : 0.005 0.060 1132 Dihedral : 3.722 17.602 870 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.38 % Allowed : 6.49 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.30), residues: 787 helix: 2.37 (0.24), residues: 461 sheet: -0.87 (0.61), residues: 61 loop : -0.52 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.010 0.001 TYR A 337 PHE 0.010 0.002 PHE B 216 TRP 0.006 0.001 TRP A 478 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 6563) covalent geometry : angle 0.56915 ( 8828) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.65500 ( 2) hydrogen bonds : bond 0.04490 ( 367) hydrogen bonds : angle 4.00544 ( 1077) *********************** 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 105 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.261 Fit side-chains REVERT: B 138 GLN cc_start: 0.8945 (mm110) cc_final: 0.8690 (mm-40) REVERT: B 224 GLU cc_start: 0.6975 (tt0) cc_final: 0.6682 (mm-30) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.0745 time to fit residues: 10.3316 Evaluate side-chains 97 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 137 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.169507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127610 restraints weight = 7501.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126682 restraints weight = 5994.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129780 restraints weight = 5502.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130031 restraints weight = 3816.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.131089 restraints weight = 3618.821| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6564 Z= 0.144 Angle : 0.499 6.119 8830 Z= 0.266 Chirality : 0.040 0.141 1008 Planarity : 0.004 0.060 1132 Dihedral : 3.641 17.137 870 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.83 % Allowed : 9.39 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.30), residues: 787 helix: 2.38 (0.24), residues: 467 sheet: -1.00 (0.59), residues: 61 loop : -0.49 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 39 TYR 0.012 0.001 TYR B 141 PHE 0.007 0.001 PHE A 310 TRP 0.004 0.001 TRP A 478 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6563) covalent geometry : angle 0.49878 ( 8828) SS BOND : bond 0.00304 ( 1) SS BOND : angle 0.57383 ( 2) hydrogen bonds : bond 0.03955 ( 367) hydrogen bonds : angle 3.78654 ( 1077) *********************** 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 105 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.249 Fit side-chains REVERT: B 138 GLN cc_start: 0.8898 (mm110) cc_final: 0.8667 (mm-40) REVERT: B 224 GLU cc_start: 0.6897 (tt0) cc_final: 0.6674 (mm-30) outliers start: 6 outliers final: 5 residues processed: 103 average time/residue: 0.0658 time to fit residues: 9.5826 Evaluate side-chains 99 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 222 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.174968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131850 restraints weight = 7671.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130433 restraints weight = 6767.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.133392 restraints weight = 6646.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133895 restraints weight = 4393.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135096 restraints weight = 4668.640| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6564 Z= 0.125 Angle : 0.482 6.224 8830 Z= 0.258 Chirality : 0.039 0.142 1008 Planarity : 0.004 0.060 1132 Dihedral : 3.552 16.415 870 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.24 % Allowed : 11.33 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.30), residues: 787 helix: 2.43 (0.24), residues: 467 sheet: -1.27 (0.59), residues: 58 loop : -0.39 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.013 0.001 TYR B 141 PHE 0.006 0.001 PHE A 310 TRP 0.003 0.000 TRP A 478 HIS 0.004 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6563) covalent geometry : angle 0.48205 ( 8828) SS BOND : bond 0.00239 ( 1) SS BOND : angle 0.49024 ( 2) hydrogen bonds : bond 0.03740 ( 367) hydrogen bonds : angle 3.70841 ( 1077) *********************** 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 107 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.199 Fit side-chains REVERT: B 98 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8028 (mt0) outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.0685 time to fit residues: 9.7641 Evaluate side-chains 98 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.174765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131052 restraints weight = 7714.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131623 restraints weight = 5868.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.133479 restraints weight = 5859.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134163 restraints weight = 3975.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136015 restraints weight = 3589.505| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1369 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= 0.126 Angle : 0.485 6.705 8830 Z= 0.259 Chirality : 0.039 0.146 1008 Planarity : 0.004 0.060 1132 Dihedral : 3.513 15.917 870 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.38 % Allowed : 12.98 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.30), residues: 787 helix: 2.44 (0.24), residues: 468 sheet: -1.28 (0.58), residues: 58 loop : -0.39 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.013 0.001 TYR B 141 PHE 0.006 0.001 PHE A 310 TRP 0.003 0.001 TRP A 478 HIS 0.005 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6563) covalent geometry : angle 0.48527 ( 8828) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.40908 ( 2) hydrogen bonds : bond 0.03645 ( 367) hydrogen bonds : angle 3.66963 ( 1077) *********************** 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 106 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.270 Fit side-chains REVERT: B 30 MET cc_start: 0.7836 (mmm) cc_final: 0.6809 (mtt) REVERT: B 98 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8014 (mt0) outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 0.0629 time to fit residues: 8.9853 Evaluate side-chains 98 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU 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 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 9 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.170257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128325 restraints weight = 7603.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127194 restraints weight = 6135.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130353 restraints weight = 5685.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130477 restraints weight = 3916.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131711 restraints weight = 3702.496| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1419 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= 0.117 Angle : 0.483 6.897 8830 Z= 0.257 Chirality : 0.039 0.178 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.469 15.531 870 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.66 % Allowed : 12.98 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.30), residues: 787 helix: 2.49 (0.24), residues: 468 sheet: -1.02 (0.64), residues: 53 loop : -0.34 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.015 0.001 TYR B 141 PHE 0.005 0.001 PHE A 310 TRP 0.002 0.000 TRP A 478 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6563) covalent geometry : angle 0.48253 ( 8828) SS BOND : bond 0.00174 ( 1) SS BOND : angle 0.34257 ( 2) hydrogen bonds : bond 0.03538 ( 367) hydrogen bonds : angle 3.64566 ( 1077) *********************** 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 104 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.329 Fit side-chains REVERT: A 349 HIS cc_start: 0.8049 (m-70) cc_final: 0.7832 (m90) REVERT: B 30 MET cc_start: 0.7872 (mmm) cc_final: 0.6884 (mtt) REVERT: B 98 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7985 (mt0) outliers start: 12 outliers final: 8 residues processed: 100 average time/residue: 0.0742 time to fit residues: 10.2098 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.125755 restraints weight = 7522.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124504 restraints weight = 6053.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126792 restraints weight = 6962.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127769 restraints weight = 4379.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.129185 restraints weight = 4044.842| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1533 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= 0.180 Angle : 0.528 6.826 8830 Z= 0.278 Chirality : 0.041 0.151 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.613 16.213 870 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.38 % Allowed : 13.81 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.30), residues: 787 helix: 2.33 (0.24), residues: 470 sheet: -1.27 (0.58), residues: 58 loop : -0.35 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.015 0.001 TYR B 141 PHE 0.009 0.001 PHE A 310 TRP 0.004 0.001 TRP A 478 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6563) covalent geometry : angle 0.52819 ( 8828) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.27976 ( 2) hydrogen bonds : bond 0.03926 ( 367) hydrogen bonds : angle 3.69781 ( 1077) *********************** 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: 10 poor density : 92 time to evaluate : 0.254 Fit side-chains REVERT: B 30 MET cc_start: 0.7981 (mmm) cc_final: 0.7270 (mtt) REVERT: B 98 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8130 (mt0) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.0732 time to fit residues: 10.1182 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 : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU 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 54 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.167820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126429 restraints weight = 7508.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124072 restraints weight = 6439.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.126918 restraints weight = 7118.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127674 restraints weight = 4255.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.129035 restraints weight = 4029.741| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6564 Z= 0.173 Angle : 0.534 7.233 8830 Z= 0.281 Chirality : 0.041 0.157 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.644 16.354 870 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.38 % Allowed : 13.54 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.30), residues: 787 helix: 2.29 (0.24), residues: 471 sheet: -1.33 (0.57), residues: 58 loop : -0.46 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.021 0.001 TYR B 141 PHE 0.005 0.001 PHE A 105 TRP 0.005 0.001 TRP A 478 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 6563) covalent geometry : angle 0.53379 ( 8828) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.32406 ( 2) hydrogen bonds : bond 0.03917 ( 367) hydrogen bonds : angle 3.71978 ( 1077) *********************** 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 102 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.218 Fit side-chains REVERT: B 30 MET cc_start: 0.7979 (mmm) cc_final: 0.7492 (mtt) REVERT: B 98 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8070 (mt0) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.0752 time to fit residues: 10.3057 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 : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU 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 39 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.171262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128867 restraints weight = 7669.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126760 restraints weight = 6176.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130613 restraints weight = 5765.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130637 restraints weight = 3958.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131898 restraints weight = 3768.709| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6564 Z= 0.144 Angle : 0.528 7.364 8830 Z= 0.278 Chirality : 0.040 0.156 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.617 15.998 870 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.24 % Allowed : 13.81 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.30), residues: 787 helix: 2.43 (0.24), residues: 465 sheet: -1.29 (0.58), residues: 58 loop : -0.36 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.020 0.001 TYR B 141 PHE 0.005 0.001 PHE B 216 TRP 0.004 0.001 TRP A 478 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6563) covalent geometry : angle 0.52771 ( 8828) SS BOND : bond 0.00129 ( 1) SS BOND : angle 0.28481 ( 2) hydrogen bonds : bond 0.03740 ( 367) hydrogen bonds : angle 3.70205 ( 1077) *********************** 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 98 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.227 Fit side-chains REVERT: B 30 MET cc_start: 0.7980 (mmm) cc_final: 0.7421 (mtt) REVERT: B 98 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8099 (mt0) outliers start: 9 outliers final: 8 residues processed: 95 average time/residue: 0.0774 time to fit residues: 10.0633 Evaluate side-chains 97 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU 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 76 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.0070 chunk 2 optimal weight: 0.2980 chunk 13 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.173611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130748 restraints weight = 7492.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131478 restraints weight = 6328.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134167 restraints weight = 5750.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134311 restraints weight = 3901.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134731 restraints weight = 3723.773| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6564 Z= 0.112 Angle : 0.517 7.647 8830 Z= 0.277 Chirality : 0.039 0.152 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.507 15.073 870 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.24 % Allowed : 14.23 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.30), residues: 787 helix: 2.53 (0.24), residues: 464 sheet: -1.03 (0.64), residues: 53 loop : -0.31 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.018 0.001 TYR B 141 PHE 0.005 0.001 PHE B 216 TRP 0.003 0.000 TRP A 478 HIS 0.009 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6563) covalent geometry : angle 0.51749 ( 8828) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.47189 ( 2) hydrogen bonds : bond 0.03437 ( 367) hydrogen bonds : angle 3.66038 ( 1077) ********************** 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 103 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.159 Fit side-chains REVERT: A 349 HIS cc_start: 0.8091 (m-70) cc_final: 0.7824 (m90) REVERT: B 30 MET cc_start: 0.7950 (mmm) cc_final: 0.7287 (mtt) REVERT: B 98 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: B 217 MET cc_start: 0.5055 (mmt) cc_final: 0.4709 (mmt) outliers start: 9 outliers final: 6 residues processed: 100 average time/residue: 0.0706 time to fit residues: 9.8257 Evaluate side-chains 96 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 244 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 48 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.171140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129885 restraints weight = 7578.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128365 restraints weight = 7042.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131381 restraints weight = 6808.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131406 restraints weight = 4557.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132209 restraints weight = 4530.712| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6564 Z= 0.143 Angle : 0.538 6.988 8830 Z= 0.287 Chirality : 0.040 0.151 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.551 15.430 870 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.97 % Allowed : 14.64 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.30), residues: 787 helix: 2.52 (0.24), residues: 463 sheet: -1.12 (0.59), residues: 58 loop : -0.32 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.019 0.001 TYR B 141 PHE 0.005 0.001 PHE B 216 TRP 0.003 0.001 TRP A 478 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6563) covalent geometry : angle 0.53849 ( 8828) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.14085 ( 2) hydrogen bonds : bond 0.03630 ( 367) hydrogen bonds : angle 3.66946 ( 1077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1056.17 seconds wall clock time: 18 minutes 51.37 seconds (1131.37 seconds total)