Starting phenix.real_space_refine on Tue Mar 11 14:30:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jfw_36218/03_2025/8jfw_36218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jfw_36218/03_2025/8jfw_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_36218/03_2025/8jfw_36218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jfw_36218/03_2025/8jfw_36218.map" model { file = "/net/cci-nas-00/data/ceres_data/8jfw_36218/03_2025/8jfw_36218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jfw_36218/03_2025/8jfw_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-5624/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: 3.56, per 1000 atoms: 0.59 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: 1.53 Conformation dependent library (CDL) restraints added in 875.4 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: 0.64 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: 1.64 Time building geometry restraints manager: 1.77 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: 0.680 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.970 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- 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 : 0.654 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: 0.1897 time to fit residues: 21.7872 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 : 0.739 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.201376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147616 restraints weight = 6757.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144585 restraints weight = 7187.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145639 restraints weight = 8070.927| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0991 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 7.966 8348 Z= 0.288 Chirality : 0.042 0.223 912 Planarity : 0.004 0.036 1099 Dihedral : 4.278 21.213 823 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.12 % Allowed : 12.86 % Favored : 85.02 % 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: 1.15 (0.32), residues: 750 helix: 1.55 (0.26), residues: 403 sheet: -0.32 (0.83), residues: 46 loop : -0.03 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 394 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 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8398 (tpp) REVERT: A 110 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6260 (mtm) outliers start: 14 outliers final: 6 residues processed: 84 average time/residue: 0.1611 time to fit residues: 18.6056 Evaluate side-chains 85 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.203298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149734 restraints weight = 6814.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146586 restraints weight = 7100.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147588 restraints weight = 8199.120| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1172 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= 0.171 Angle : 0.485 7.786 8348 Z= 0.258 Chirality : 0.041 0.218 912 Planarity : 0.003 0.027 1099 Dihedral : 4.129 18.386 823 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.36 % Allowed : 14.83 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.31), residues: 750 helix: 1.64 (0.27), residues: 399 sheet: 0.07 (0.75), residues: 56 loop : -0.13 (0.37), residues: 295 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 0.012 0.001 PHE D 535 TYR 0.011 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 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6018 (mtm) REVERT: D 47 GLU cc_start: 0.8255 (pp20) cc_final: 0.8034 (pp20) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.1586 time to fit residues: 19.3087 Evaluate side-chains 86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 469 VAL 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 14 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 20 optimal weight: 0.0000 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.204993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153038 restraints weight = 6917.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151499 restraints weight = 8424.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152919 restraints weight = 7935.503| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6187 Z= 0.149 Angle : 0.466 6.347 8348 Z= 0.247 Chirality : 0.040 0.214 912 Planarity : 0.003 0.031 1099 Dihedral : 3.981 18.314 823 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.82 % Allowed : 14.22 % Favored : 83.96 % 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: 1.22 (0.31), residues: 750 helix: 1.72 (0.27), residues: 398 sheet: 0.03 (0.72), residues: 62 loop : -0.23 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 15 HIS 0.004 0.000 HIS D 271 PHE 0.009 0.001 PHE D 347 TYR 0.010 0.001 TYR D 394 ARG 0.002 0.000 ARG D 440 *********************** 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 97 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7281 (mt-10) REVERT: A 72 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8206 (tpp) REVERT: A 110 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6116 (mtm) REVERT: D 47 GLU cc_start: 0.8199 (pp20) cc_final: 0.7899 (pp20) REVERT: D 470 MET cc_start: 0.8776 (tpp) cc_final: 0.8528 (mmm) REVERT: D 521 MET cc_start: 0.6138 (mtp) cc_final: 0.5713 (mmm) outliers start: 12 outliers final: 6 residues processed: 92 average time/residue: 0.1527 time to fit residues: 19.6857 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 D residue 432 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.204130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152071 restraints weight = 6866.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150141 restraints weight = 8006.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151323 restraints weight = 8403.207| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6187 Z= 0.154 Angle : 0.462 6.990 8348 Z= 0.245 Chirality : 0.040 0.216 912 Planarity : 0.003 0.033 1099 Dihedral : 3.917 18.245 823 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.27 % Allowed : 13.92 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.27), residues: 399 sheet: 0.12 (0.76), residues: 56 loop : -0.14 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 15 HIS 0.003 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 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 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 110 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6072 (mtm) REVERT: D 47 GLU cc_start: 0.8187 (pp20) cc_final: 0.7845 (pp20) REVERT: D 470 MET cc_start: 0.8824 (tpp) cc_final: 0.8563 (mmm) REVERT: D 521 MET cc_start: 0.6143 (mtp) cc_final: 0.5727 (mmm) outliers start: 15 outliers final: 9 residues processed: 94 average time/residue: 0.1600 time to fit residues: 20.8085 Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 432 LEU 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 48 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 0.0170 overall best weight: 0.7022 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.204015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150938 restraints weight = 6693.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147517 restraints weight = 7015.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149371 restraints weight = 7736.422| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6187 Z= 0.161 Angle : 0.480 8.060 8348 Z= 0.251 Chirality : 0.040 0.217 912 Planarity : 0.003 0.035 1099 Dihedral : 3.923 17.900 823 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.97 % Allowed : 14.98 % Favored : 83.06 % 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: 1.32 (0.31), residues: 750 helix: 1.79 (0.27), residues: 397 sheet: 0.06 (0.76), residues: 56 loop : -0.15 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 15 HIS 0.003 0.001 HIS D 271 PHE 0.010 0.001 PHE D 347 TYR 0.010 0.001 TYR D 394 ARG 0.001 0.000 ARG D 358 *********************** 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 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 110 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6139 (mtm) REVERT: D 47 GLU cc_start: 0.8201 (pp20) cc_final: 0.7831 (pp20) REVERT: D 251 ASP cc_start: 0.7981 (t70) cc_final: 0.7763 (t70) REVERT: D 470 MET cc_start: 0.8848 (tpp) cc_final: 0.8536 (mmm) REVERT: D 521 MET cc_start: 0.6206 (mtp) cc_final: 0.5789 (mmm) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.1516 time to fit residues: 19.5571 Evaluate side-chains 92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 110 MET 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 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 23 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.199459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146620 restraints weight = 6857.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147302 restraints weight = 7791.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147736 restraints weight = 6669.131| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6187 Z= 0.300 Angle : 0.548 8.791 8348 Z= 0.287 Chirality : 0.043 0.242 912 Planarity : 0.003 0.035 1099 Dihedral : 4.203 19.691 823 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.27 % Allowed : 15.28 % Favored : 82.45 % 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: 1.07 (0.31), residues: 750 helix: 1.60 (0.26), residues: 402 sheet: -0.46 (0.79), residues: 51 loop : -0.23 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 318 HIS 0.007 0.001 HIS D 271 PHE 0.018 0.002 PHE D 347 TYR 0.013 0.001 TYR D 394 ARG 0.003 0.000 ARG D 27 *********************** 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 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6282 (mtm) REVERT: D 47 GLU cc_start: 0.8273 (pp20) cc_final: 0.7895 (pp20) REVERT: D 447 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8818 (tt0) REVERT: D 521 MET cc_start: 0.6305 (mtp) cc_final: 0.6013 (mmm) outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 0.1618 time to fit residues: 19.6173 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 47 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.201840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149403 restraints weight = 6743.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144511 restraints weight = 8060.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147129 restraints weight = 7895.419| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1708 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 : 0.492 8.907 8348 Z= 0.257 Chirality : 0.041 0.220 912 Planarity : 0.003 0.035 1099 Dihedral : 4.039 20.612 823 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.82 % Allowed : 15.73 % Favored : 82.45 % 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: 1.12 (0.31), residues: 750 helix: 1.64 (0.26), residues: 403 sheet: -0.27 (0.78), residues: 53 loop : -0.24 (0.36), residues: 294 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 0.011 0.001 PHE D 347 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 96 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7817 (tpp) REVERT: A 73 MET cc_start: 0.8138 (mmm) cc_final: 0.7784 (tpt) REVERT: A 110 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6211 (mtm) REVERT: D 47 GLU cc_start: 0.8248 (pp20) cc_final: 0.7861 (pp20) REVERT: D 251 ASP cc_start: 0.8047 (t70) cc_final: 0.7837 (t70) REVERT: D 470 MET cc_start: 0.8683 (mmm) cc_final: 0.8452 (mmt) outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 0.1662 time to fit residues: 20.6847 Evaluate side-chains 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 110 MET 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 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 73 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.202479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150105 restraints weight = 6847.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147046 restraints weight = 7659.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.148529 restraints weight = 7784.459| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6187 Z= 0.177 Angle : 0.498 10.182 8348 Z= 0.258 Chirality : 0.041 0.218 912 Planarity : 0.003 0.036 1099 Dihedral : 3.993 19.923 823 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.82 % Allowed : 16.04 % 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: 1.16 (0.31), residues: 750 helix: 1.66 (0.26), residues: 404 sheet: -0.23 (0.79), residues: 53 loop : -0.23 (0.36), residues: 293 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 0.011 0.001 PHE A 90 TYR 0.010 0.001 TYR D 394 ARG 0.002 0.000 ARG D 358 *********************** 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 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6235 (mtm) REVERT: D 47 GLU cc_start: 0.8248 (pp20) cc_final: 0.7857 (pp20) REVERT: D 447 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8796 (tt0) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.1596 time to fit residues: 19.2284 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.199501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.146845 restraints weight = 6831.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143451 restraints weight = 7115.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144966 restraints weight = 7304.967| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6187 Z= 0.249 Angle : 0.535 11.126 8348 Z= 0.277 Chirality : 0.042 0.226 912 Planarity : 0.003 0.035 1099 Dihedral : 4.114 20.401 823 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.82 % Allowed : 15.89 % 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: 1.06 (0.31), residues: 750 helix: 1.59 (0.26), residues: 404 sheet: -0.35 (0.79), residues: 53 loop : -0.27 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 318 HIS 0.006 0.001 HIS D 271 PHE 0.015 0.001 PHE D 347 TYR 0.012 0.001 TYR D 394 ARG 0.003 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 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.8119 (mmm) cc_final: 0.7810 (tpt) REVERT: A 110 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6249 (mtm) REVERT: D 47 GLU cc_start: 0.8272 (pp20) cc_final: 0.7875 (pp20) REVERT: D 447 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8823 (tt0) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.1733 time to fit residues: 21.0060 Evaluate side-chains 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 110 MET 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 548 LEU 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 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.201772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148293 restraints weight = 6838.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143844 restraints weight = 6663.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144590 restraints weight = 8006.073| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6187 Z= 0.172 Angle : 0.499 11.209 8348 Z= 0.258 Chirality : 0.041 0.220 912 Planarity : 0.003 0.035 1099 Dihedral : 3.975 19.906 823 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.51 % Allowed : 16.49 % 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: 1.15 (0.31), residues: 750 helix: 1.67 (0.26), residues: 404 sheet: -0.32 (0.80), residues: 53 loop : -0.23 (0.36), residues: 293 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 0.010 0.001 PHE A 142 TYR 0.010 0.001 TYR D 394 ARG 0.002 0.000 ARG D 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.20 seconds wall clock time: 33 minutes 28.70 seconds (2008.70 seconds total)