Starting phenix.real_space_refine on Fri Dec 27 16:54:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jfw_36218/12_2024/8jfw_36218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jfw_36218/12_2024/8jfw_36218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jfw_36218/12_2024/8jfw_36218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jfw_36218/12_2024/8jfw_36218.map" model { file = "/net/cci-nas-00/data/ceres_data/8jfw_36218/12_2024/8jfw_36218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jfw_36218/12_2024/8jfw_36218.cif" } resolution = 3.64 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 S 33 5.16 5 C 3820 2.51 5 N 1058 2.21 5 O 1163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6076 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1109 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 4965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4965 Classifications: {'peptide': 613} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.25, per 1000 atoms: 0.70 Number of scatterers: 6076 At special positions: 0 Unit cell: (74.385, 85.5, 103.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 33 16.00 O 1163 8.00 N 1058 7.00 C 3820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 843.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 271 " 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 57.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 removed outlier: 4.060A pdb=" N LYS A 14 " --> pdb=" O ILE A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.858A pdb=" N ARG A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 84 through 92 removed outlier: 4.239A pdb=" N GLU A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.609A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 112 " --> pdb=" O HIS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.736A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'D' and resid 2 through 46 Processing helix chain 'D' and resid 46 through 59 removed outlier: 4.017A pdb=" N LYS D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 114 removed outlier: 3.739A pdb=" N ILE D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 114 " --> pdb=" O ASP D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 137 removed outlier: 3.645A pdb=" N LYS D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 194 through 209 removed outlier: 3.711A pdb=" N VAL D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.677A pdb=" N ALA D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 242 through 256 removed outlier: 3.566A pdb=" N ARG D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 285 through 286 No H-bonds generated for 'chain 'D' and resid 285 through 286' Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 306 through 319 removed outlier: 3.834A pdb=" N TRP D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 352 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 419 through 440 removed outlier: 3.928A pdb=" N VAL D 427 " --> pdb=" O ARG D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 453 Processing helix chain 'D' and resid 463 through 475 Processing helix chain 'D' and resid 479 through 482 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 498 through 506 removed outlier: 3.618A pdb=" N LEU D 505 " --> pdb=" O THR D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 517 removed outlier: 3.832A pdb=" N ASP D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 527 Processing helix chain 'D' and resid 527 through 538 removed outlier: 3.783A pdb=" N LEU D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 562 removed outlier: 3.550A pdb=" N HIS D 561 " --> pdb=" O LEU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 Processing helix chain 'D' and resid 587 through 612 removed outlier: 4.418A pdb=" N ALA D 594 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'D' and resid 142 through 145 removed outlier: 6.905A pdb=" N LEU D 268 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 213 through 215 Processing sheet with id=AA4, first strand: chain 'D' and resid 320 through 321 Processing sheet with id=AA5, first strand: chain 'D' and resid 460 through 462 311 hydrogen bonds defined for protein. 906 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: 1.72 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2069 1.35 - 1.46: 1341 1.46 - 1.58: 2717 1.58 - 1.70: 1 1.70 - 1.82: 59 Bond restraints: 6187 Sorted by residual: bond pdb=" CB PRO D 329 " pdb=" CG PRO D 329 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.65e+00 bond pdb=" CA ASP D 190 " pdb=" CB ASP D 190 " ideal model delta sigma weight residual 1.532 1.548 -0.016 1.33e-02 5.65e+03 1.42e+00 bond pdb=" N ASP D 457 " pdb=" CA ASP D 457 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.48e-01 bond pdb=" CB MET A 145 " pdb=" CG MET A 145 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.36e-01 bond pdb=" CB GLU A 128 " pdb=" CG GLU A 128 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.16e-01 ... (remaining 6182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 8253 2.28 - 4.55: 85 4.55 - 6.83: 5 6.83 - 9.11: 2 9.11 - 11.39: 3 Bond angle restraints: 8348 Sorted by residual: angle pdb=" CA PRO D 329 " pdb=" N PRO D 329 " pdb=" CD PRO D 329 " ideal model delta sigma weight residual 112.00 102.42 9.58 1.40e+00 5.10e-01 4.68e+01 angle pdb=" CB MET D 424 " pdb=" CG MET D 424 " pdb=" SD MET D 424 " ideal model delta sigma weight residual 112.70 124.09 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CB MET A 145 " pdb=" CG MET A 145 " pdb=" SD MET A 145 " ideal model delta sigma weight residual 112.70 123.21 -10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N ASN D 536 " pdb=" CA ASN D 536 " pdb=" C ASN D 536 " ideal model delta sigma weight residual 113.41 109.66 3.75 1.22e+00 6.72e-01 9.44e+00 angle pdb=" CA MET A 145 " pdb=" CB MET A 145 " pdb=" CG MET A 145 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 ... (remaining 8343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3336 17.96 - 35.93: 347 35.93 - 53.89: 72 53.89 - 71.86: 11 71.86 - 89.82: 5 Dihedral angle restraints: 3771 sinusoidal: 1564 harmonic: 2207 Sorted by residual: dihedral pdb=" CA PHE D 188 " pdb=" C PHE D 188 " pdb=" N VAL D 189 " pdb=" CA VAL D 189 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA VAL D 189 " pdb=" C VAL D 189 " pdb=" N ASP D 190 " pdb=" CA ASP D 190 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ILE A 126 " pdb=" C ILE A 126 " pdb=" N ARG A 127 " pdb=" CA ARG A 127 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 3768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 689 0.040 - 0.081: 160 0.081 - 0.121: 56 0.121 - 0.161: 5 0.161 - 0.201: 2 Chirality restraints: 912 Sorted by residual: chirality pdb=" CB VAL D 189 " pdb=" CA VAL D 189 " pdb=" CG1 VAL D 189 " pdb=" CG2 VAL D 189 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASP D 190 " pdb=" N ASP D 190 " pdb=" C ASP D 190 " pdb=" CB ASP D 190 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA PRO D 329 " pdb=" N PRO D 329 " pdb=" C PRO D 329 " pdb=" CB PRO D 329 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 909 not shown) Planarity restraints: 1099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 328 " -0.069 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO D 329 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO D 329 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 329 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 189 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C VAL D 189 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL D 189 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP D 190 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 43 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 44 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " -0.017 5.00e-02 4.00e+02 ... (remaining 1096 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 57 2.60 - 3.18: 5194 3.18 - 3.75: 9274 3.75 - 4.33: 11975 4.33 - 4.90: 20400 Nonbonded interactions: 46900 Sorted by model distance: nonbonded pdb=" OD1 ASN D 219 " pdb="ZN ZN D 702 " model vdw 2.029 2.230 nonbonded pdb=" OD2 ASP D 187 " pdb="ZN ZN D 702 " model vdw 2.070 2.230 nonbonded pdb=" OG1 THR D 547 " pdb=" OD1 ASP D 549 " model vdw 2.111 3.040 nonbonded pdb=" OD2 ASP D 187 " pdb="FE FE D 701 " model vdw 2.118 2.260 nonbonded pdb=" NE2 HIS D 160 " pdb="FE FE D 701 " model vdw 2.176 2.340 ... (remaining 46895 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 19.060 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 0.108 6187 Z= 0.186 Angle : 0.603 11.386 8348 Z= 0.350 Chirality : 0.040 0.201 912 Planarity : 0.004 0.098 1099 Dihedral : 15.174 89.824 2339 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.15 % Allowed : 14.67 % Favored : 85.17 % 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: 1.30 (0.31), residues: 750 helix: 1.78 (0.27), residues: 379 sheet: -0.09 (0.65), residues: 63 loop : -0.01 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 15 HIS 0.002 0.000 HIS D 271 PHE 0.010 0.001 PHE D 535 TYR 0.006 0.001 TYR D 394 ARG 0.006 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.7873 (p90) cc_final: 0.7295 (p90) REVERT: D 498 TYR cc_start: 0.7701 (p90) cc_final: 0.7253 (p90) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1767 time to fit residues: 20.2712 Evaluate side-chains 81 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6187 Z= 0.236 Angle : 0.537 7.929 8348 Z= 0.288 Chirality : 0.042 0.220 912 Planarity : 0.004 0.036 1099 Dihedral : 4.283 21.132 823 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.12 % Allowed : 13.01 % Favored : 84.87 % 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: 1.14 (0.32), residues: 750 helix: 1.54 (0.26), residues: 403 sheet: -0.33 (0.83), residues: 46 loop : -0.04 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 318 HIS 0.005 0.001 HIS D 271 PHE 0.014 0.001 PHE D 347 TYR 0.011 0.001 TYR D 254 ARG 0.004 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6259 (mtm) outliers start: 14 outliers final: 6 residues processed: 85 average time/residue: 0.1843 time to fit residues: 21.2677 Evaluate side-chains 85 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN D 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6187 Z= 0.252 Angle : 0.529 7.670 8348 Z= 0.281 Chirality : 0.042 0.226 912 Planarity : 0.003 0.029 1099 Dihedral : 4.342 19.514 823 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.97 % Allowed : 13.62 % Favored : 84.42 % 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: 1.01 (0.31), residues: 750 helix: 1.52 (0.26), residues: 402 sheet: -0.63 (0.83), residues: 46 loop : -0.19 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 318 HIS 0.006 0.001 HIS D 271 PHE 0.016 0.001 PHE D 347 TYR 0.012 0.001 TYR D 394 ARG 0.003 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6072 (mtm) outliers start: 13 outliers final: 11 residues processed: 86 average time/residue: 0.1645 time to fit residues: 19.8509 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 548 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.0170 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6187 Z= 0.166 Angle : 0.476 6.047 8348 Z= 0.254 Chirality : 0.040 0.216 912 Planarity : 0.003 0.032 1099 Dihedral : 4.118 19.651 823 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.97 % Allowed : 13.92 % Favored : 84.11 % 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: 1.10 (0.31), residues: 750 helix: 1.66 (0.27), residues: 397 sheet: -0.23 (0.71), residues: 62 loop : -0.27 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 15 HIS 0.004 0.001 HIS D 271 PHE 0.010 0.001 PHE D 347 TYR 0.010 0.001 TYR D 394 ARG 0.002 0.000 ARG D 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8225 (tpp) REVERT: A 110 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6108 (mtm) REVERT: D 47 GLU cc_start: 0.8349 (pp20) cc_final: 0.7930 (pp20) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 0.1695 time to fit residues: 21.5086 Evaluate side-chains 88 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 0.0030 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6187 Z= 0.164 Angle : 0.469 6.776 8348 Z= 0.248 Chirality : 0.040 0.217 912 Planarity : 0.003 0.031 1099 Dihedral : 4.015 19.068 823 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.66 % Allowed : 14.98 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.31), residues: 750 helix: 1.69 (0.27), residues: 399 sheet: -0.11 (0.77), residues: 56 loop : -0.28 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 15 HIS 0.004 0.001 HIS D 271 PHE 0.010 0.001 PHE D 347 TYR 0.010 0.001 TYR D 394 ARG 0.003 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.6418 (ptp) cc_final: 0.6181 (mtm) REVERT: D 47 GLU cc_start: 0.8328 (pp20) cc_final: 0.7881 (pp20) REVERT: D 447 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8841 (tt0) outliers start: 11 outliers final: 7 residues processed: 90 average time/residue: 0.1641 time to fit residues: 20.7196 Evaluate side-chains 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6187 Z= 0.204 Angle : 0.490 8.051 8348 Z= 0.259 Chirality : 0.041 0.222 912 Planarity : 0.003 0.033 1099 Dihedral : 4.052 18.807 823 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.12 % Allowed : 14.98 % Favored : 82.90 % 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: 1.11 (0.31), residues: 750 helix: 1.63 (0.26), residues: 405 sheet: -0.23 (0.75), residues: 56 loop : -0.28 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 15 HIS 0.005 0.001 HIS D 271 PHE 0.013 0.001 PHE D 347 TYR 0.011 0.001 TYR D 394 ARG 0.003 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.7389 (mtt) cc_final: 0.6800 (mtt) REVERT: A 72 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7832 (tpp) REVERT: D 447 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8847 (tt0) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.1537 time to fit residues: 18.3157 Evaluate side-chains 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 0.0470 chunk 52 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6187 Z= 0.150 Angle : 0.478 8.816 8348 Z= 0.248 Chirality : 0.040 0.217 912 Planarity : 0.003 0.035 1099 Dihedral : 3.931 18.853 823 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.12 % Allowed : 15.13 % Favored : 82.75 % 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: 1.20 (0.31), residues: 750 helix: 1.74 (0.27), residues: 400 sheet: -0.15 (0.76), residues: 56 loop : -0.26 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 15 HIS 0.003 0.001 HIS D 271 PHE 0.014 0.001 PHE A 17 TYR 0.010 0.001 TYR D 394 ARG 0.002 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7450 (mt-10) REVERT: D 447 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8856 (tt0) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.2044 time to fit residues: 25.6855 Evaluate side-chains 92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 578 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 63 optimal weight: 0.0470 chunk 67 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6187 Z= 0.146 Angle : 0.478 9.227 8348 Z= 0.247 Chirality : 0.040 0.216 912 Planarity : 0.003 0.036 1099 Dihedral : 3.870 18.528 823 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.12 % Allowed : 15.58 % Favored : 82.30 % 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: 1.26 (0.31), residues: 750 helix: 1.80 (0.27), residues: 400 sheet: -0.11 (0.76), residues: 56 loop : -0.26 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 15 HIS 0.003 0.000 HIS D 271 PHE 0.010 0.001 PHE A 90 TYR 0.010 0.001 TYR D 394 ARG 0.002 0.000 ARG D 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 52 MET cc_start: 0.7304 (mtt) cc_final: 0.6714 (mtt) REVERT: A 72 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7797 (tpp) REVERT: A 73 MET cc_start: 0.8145 (mmm) cc_final: 0.7788 (tpt) REVERT: A 139 TYR cc_start: 0.7993 (p90) cc_final: 0.7433 (p90) REVERT: D 47 GLU cc_start: 0.8312 (pp20) cc_final: 0.7839 (pp20) REVERT: D 447 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8844 (tt0) outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 0.1778 time to fit residues: 23.5908 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 578 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6187 Z= 0.142 Angle : 0.489 10.151 8348 Z= 0.251 Chirality : 0.040 0.221 912 Planarity : 0.003 0.036 1099 Dihedral : 3.865 19.481 823 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.82 % Allowed : 16.19 % Favored : 82.00 % 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: 1.29 (0.31), residues: 750 helix: 1.80 (0.27), residues: 401 sheet: -0.11 (0.77), residues: 56 loop : -0.21 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 15 HIS 0.003 0.000 HIS D 271 PHE 0.011 0.001 PHE A 142 TYR 0.009 0.001 TYR D 394 ARG 0.002 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 73 MET cc_start: 0.8065 (mmm) cc_final: 0.7724 (tpt) REVERT: A 139 TYR cc_start: 0.7992 (p90) cc_final: 0.7482 (p90) REVERT: D 47 GLU cc_start: 0.8288 (pp20) cc_final: 0.7875 (mm-30) REVERT: D 447 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8864 (tt0) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 0.1527 time to fit residues: 21.0813 Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 578 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6187 Z= 0.184 Angle : 0.511 11.184 8348 Z= 0.264 Chirality : 0.041 0.225 912 Planarity : 0.003 0.035 1099 Dihedral : 3.932 19.976 823 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.21 % Allowed : 16.64 % Favored : 82.15 % 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: 1.24 (0.31), residues: 750 helix: 1.76 (0.27), residues: 402 sheet: -0.13 (0.77), residues: 56 loop : -0.24 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 15 HIS 0.004 0.001 HIS D 271 PHE 0.011 0.001 PHE D 347 TYR 0.010 0.001 TYR D 394 ARG 0.002 0.000 ARG D 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 139 TYR cc_start: 0.8019 (p90) cc_final: 0.7530 (p90) REVERT: D 447 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8853 (tt0) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.1691 time to fit residues: 20.9228 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 578 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.203405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150514 restraints weight = 6859.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150306 restraints weight = 7761.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.150800 restraints weight = 6930.322| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6187 Z= 0.182 Angle : 0.509 11.465 8348 Z= 0.263 Chirality : 0.041 0.216 912 Planarity : 0.003 0.035 1099 Dihedral : 3.907 20.436 823 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.36 % Allowed : 16.64 % Favored : 82.00 % 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: 1.20 (0.31), residues: 750 helix: 1.74 (0.26), residues: 402 sheet: -0.13 (0.77), residues: 56 loop : -0.29 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 15 HIS 0.004 0.001 HIS D 271 PHE 0.012 0.001 PHE A 17 TYR 0.010 0.001 TYR D 394 ARG 0.002 0.000 ARG D 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.75 seconds wall clock time: 27 minutes 16.84 seconds (1636.84 seconds total)