Starting phenix.real_space_refine on Thu Nov 14 07:36:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kep_37163/11_2024/8kep_37163.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kep_37163/11_2024/8kep_37163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kep_37163/11_2024/8kep_37163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kep_37163/11_2024/8kep_37163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kep_37163/11_2024/8kep_37163.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kep_37163/11_2024/8kep_37163.cif" } resolution = 2.93 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= 0.012 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3060 2.51 5 N 825 2.21 5 O 928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4834 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1615 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "L" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1645 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "A" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1574 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Time building chain proxies: 4.02, per 1000 atoms: 0.83 Number of scatterers: 4834 At special positions: 0 Unit cell: (74.97, 72.59, 138.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 928 8.00 N 825 7.00 C 3060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 604.0 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1154 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 13 sheets defined 4.3% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.809A pdb=" N ALA A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.565A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.534A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR H 80 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.890A pdb=" N TRP H 50 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.506A pdb=" N SER H 128 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS H 151 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 132 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER H 188 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 189 " --> pdb=" O HIS H 172 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS H 172 " --> pdb=" O VAL H 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 158 through 162 removed outlier: 3.612A pdb=" N THR H 159 " --> pdb=" O ASN H 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 177 through 178 removed outlier: 3.737A pdb=" N VAL H 177 " --> pdb=" O SER H 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.628A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.678A pdb=" N GLU L 106 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR L 103 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.871A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.720A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.875A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR L 198 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN L 148 " --> pdb=" O GLU L 196 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.747A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 108 hydrogen bonds defined for protein. 276 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: 1.22 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1552 1.34 - 1.46: 1239 1.46 - 1.58: 2144 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 4959 Sorted by residual: bond pdb=" C SER L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 1.335 1.354 -0.019 8.70e-03 1.32e+04 4.65e+00 bond pdb=" C LYS H 209 " pdb=" N PRO H 210 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C TYR A 489 " pdb=" N PHE A 490 " ideal model delta sigma weight residual 1.332 1.353 -0.022 1.92e-02 2.71e+03 1.28e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" C THR L 179 " pdb=" N LEU L 180 " ideal model delta sigma weight residual 1.331 1.342 -0.012 1.29e-02 6.01e+03 8.63e-01 ... (remaining 4954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 6332 1.15 - 2.30: 313 2.30 - 3.46: 82 3.46 - 4.61: 14 4.61 - 5.76: 10 Bond angle restraints: 6751 Sorted by residual: angle pdb=" N TRP H 47 " pdb=" CA TRP H 47 " pdb=" C TRP H 47 " ideal model delta sigma weight residual 108.45 113.85 -5.40 1.26e+00 6.30e-01 1.84e+01 angle pdb=" N ILE A 418 " pdb=" CA ILE A 418 " pdb=" C ILE A 418 " ideal model delta sigma weight residual 112.29 108.26 4.03 9.40e-01 1.13e+00 1.84e+01 angle pdb=" N ASP H 66 " pdb=" CA ASP H 66 " pdb=" C ASP H 66 " ideal model delta sigma weight residual 114.56 109.22 5.34 1.27e+00 6.20e-01 1.77e+01 angle pdb=" N GLU L 82 " pdb=" CA GLU L 82 " pdb=" C GLU L 82 " ideal model delta sigma weight residual 114.09 108.85 5.24 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N SER H 122 " pdb=" CA SER H 122 " pdb=" C SER H 122 " ideal model delta sigma weight residual 107.73 111.58 -3.85 1.34e+00 5.57e-01 8.27e+00 ... (remaining 6746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 2830 17.00 - 33.99: 100 33.99 - 50.99: 17 50.99 - 67.98: 5 67.98 - 84.98: 3 Dihedral angle restraints: 2955 sinusoidal: 1149 harmonic: 1806 Sorted by residual: dihedral pdb=" CA GLU L 80 " pdb=" C GLU L 80 " pdb=" N PRO L 81 " pdb=" CA PRO L 81 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU H 156 " pdb=" C GLU H 156 " pdb=" N PRO H 157 " pdb=" CA PRO H 157 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" SG CYS H 101 " pdb=" CB CYS H 106 " pdb=" SG CYS H 106 " pdb=" CA CYS H 106 " ideal model delta sinusoidal sigma weight residual -73.00 0.62 -73.62 1 2.00e+01 2.50e-03 1.72e+01 ... (remaining 2952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 431 0.026 - 0.051: 176 0.051 - 0.077: 60 0.077 - 0.102: 54 0.102 - 0.128: 20 Chirality restraints: 741 Sorted by residual: chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL H 129 " pdb=" N VAL H 129 " pdb=" C VAL H 129 " pdb=" CB VAL H 129 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 738 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO H 14 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 373 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO H 157 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " 0.018 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1606 2.84 - 3.36: 3821 3.36 - 3.87: 7271 3.87 - 4.39: 7869 4.39 - 4.90: 14182 Nonbonded interactions: 34749 Sorted by model distance: nonbonded pdb=" OE1 GLU L 196 " pdb=" OG1 THR L 207 " model vdw 2.328 3.040 nonbonded pdb=" NH1 ARG H 12 " pdb=" O SER H 17 " model vdw 2.337 3.120 nonbonded pdb=" OE2 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.373 3.120 nonbonded pdb=" NZ LYS H 19 " pdb=" OE2 GLU H 82 " model vdw 2.425 3.120 nonbonded pdb=" O PRO H 193 " pdb=" OG SER H 196 " model vdw 2.430 3.040 ... (remaining 34744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.130 Find NCS groups from input model: 0.070 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:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.002 0.038 4959 Z= 0.148 Angle : 0.638 5.760 6751 Z= 0.393 Chirality : 0.041 0.128 741 Planarity : 0.004 0.047 873 Dihedral : 8.962 84.975 1774 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 2.78 % Allowed : 6.68 % Favored : 90.54 % 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: -4.25 (0.30), residues: 616 helix: -4.63 (0.37), residues: 40 sheet: -1.63 (0.32), residues: 235 loop : -3.62 (0.28), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.001 0.000 HIS H 100 PHE 0.005 0.001 PHE L 140 TYR 0.007 0.001 TYR L 92 ARG 0.002 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.707 Fit side-chains REVERT: H 4 LEU cc_start: 0.7747 (mp) cc_final: 0.7456 (mp) REVERT: H 55 SER cc_start: 0.7961 (t) cc_final: 0.7701 (t) REVERT: H 117 THR cc_start: 0.7706 (m) cc_final: 0.7447 (p) REVERT: L 68 SER cc_start: 0.8073 (p) cc_final: 0.7861 (m) REVERT: L 90 GLN cc_start: 0.8353 (tt0) cc_final: 0.8089 (tt0) REVERT: L 127 LYS cc_start: 0.8929 (mttt) cc_final: 0.8667 (mttt) REVERT: L 133 VAL cc_start: 0.8302 (t) cc_final: 0.8017 (m) REVERT: L 209 SER cc_start: 0.7999 (p) cc_final: 0.7779 (t) REVERT: A 334 ASN cc_start: 0.6235 (p0) cc_final: 0.5833 (t160) outliers start: 15 outliers final: 1 residues processed: 140 average time/residue: 0.9235 time to fit residues: 135.9500 Evaluate side-chains 101 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.0170 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN H 100 HIS H 105 ASN H 107 HIS H 179 GLN L 6 GLN L 39 GLN L 90 GLN L 101 GLN A 414 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4959 Z= 0.245 Angle : 0.684 12.222 6751 Z= 0.341 Chirality : 0.046 0.147 741 Planarity : 0.005 0.047 873 Dihedral : 4.422 26.277 684 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 4.64 % Allowed : 15.03 % Favored : 80.33 % 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: -3.43 (0.31), residues: 616 helix: -3.99 (0.58), residues: 34 sheet: -0.67 (0.35), residues: 217 loop : -3.33 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 436 HIS 0.003 0.001 HIS H 172 PHE 0.016 0.002 PHE L 210 TYR 0.014 0.002 TYR L 50 ARG 0.006 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.497 Fit side-chains REVERT: H 4 LEU cc_start: 0.7984 (mp) cc_final: 0.7688 (mp) REVERT: H 55 SER cc_start: 0.8034 (t) cc_final: 0.7797 (t) REVERT: H 58 THR cc_start: 0.8207 (p) cc_final: 0.7911 (p) REVERT: L 81 PRO cc_start: 0.8243 (Cg_endo) cc_final: 0.8043 (Cg_exo) REVERT: L 90 GLN cc_start: 0.8277 (tt0) cc_final: 0.7947 (tt0) REVERT: L 108 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7854 (mtpp) REVERT: L 109 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7040 (ttp80) REVERT: L 127 LYS cc_start: 0.8900 (mttt) cc_final: 0.8600 (mttt) REVERT: L 133 VAL cc_start: 0.8443 (t) cc_final: 0.8166 (m) REVERT: L 143 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7246 (tpt-90) REVERT: L 209 SER cc_start: 0.7866 (p) cc_final: 0.7534 (t) REVERT: A 334 ASN cc_start: 0.6498 (p0) cc_final: 0.5918 (t160) REVERT: A 386 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6243 (pttt) outliers start: 25 outliers final: 9 residues processed: 119 average time/residue: 0.8952 time to fit residues: 112.2582 Evaluate side-chains 109 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.0010 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4959 Z= 0.191 Angle : 0.655 10.804 6751 Z= 0.321 Chirality : 0.045 0.146 741 Planarity : 0.004 0.048 873 Dihedral : 4.448 25.689 684 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 4.27 % Allowed : 18.00 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.32), residues: 616 helix: -3.56 (0.70), residues: 34 sheet: -0.28 (0.36), residues: 219 loop : -3.15 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS H 172 PHE 0.015 0.001 PHE L 210 TYR 0.012 0.001 TYR A 501 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.591 Fit side-chains REVERT: H 58 THR cc_start: 0.8246 (p) cc_final: 0.7957 (p) REVERT: L 81 PRO cc_start: 0.8154 (Cg_endo) cc_final: 0.7874 (Cg_exo) REVERT: L 90 GLN cc_start: 0.8139 (tt0) cc_final: 0.7857 (tt0) REVERT: L 108 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7833 (mtpp) REVERT: L 109 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7174 (ttp80) REVERT: L 127 LYS cc_start: 0.8895 (mttt) cc_final: 0.8597 (mttt) REVERT: L 209 SER cc_start: 0.7742 (p) cc_final: 0.7428 (t) REVERT: A 358 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7576 (mp) outliers start: 23 outliers final: 10 residues processed: 116 average time/residue: 0.9796 time to fit residues: 119.0310 Evaluate side-chains 109 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.0030 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4959 Z= 0.236 Angle : 0.693 10.681 6751 Z= 0.342 Chirality : 0.046 0.182 741 Planarity : 0.004 0.049 873 Dihedral : 4.705 26.591 684 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 4.82 % Allowed : 19.48 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.32), residues: 616 helix: -3.38 (0.74), residues: 34 sheet: -0.04 (0.36), residues: 219 loop : -3.04 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 149 HIS 0.002 0.000 HIS H 172 PHE 0.018 0.001 PHE A 456 TYR 0.013 0.002 TYR L 174 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.551 Fit side-chains REVERT: H 58 THR cc_start: 0.8321 (p) cc_final: 0.8056 (p) REVERT: L 6 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: L 10 THR cc_start: 0.8241 (p) cc_final: 0.7832 (m) REVERT: L 90 GLN cc_start: 0.8135 (tt0) cc_final: 0.7897 (tt0) REVERT: L 105 VAL cc_start: 0.8137 (t) cc_final: 0.7924 (m) REVERT: L 109 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7113 (ttp80) REVERT: L 127 LYS cc_start: 0.8904 (mttt) cc_final: 0.8597 (mttt) REVERT: L 147 VAL cc_start: 0.9133 (m) cc_final: 0.8875 (p) REVERT: L 175 SER cc_start: 0.8314 (t) cc_final: 0.7818 (p) REVERT: L 209 SER cc_start: 0.7721 (p) cc_final: 0.7401 (t) REVERT: A 386 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6311 (pttt) outliers start: 26 outliers final: 15 residues processed: 117 average time/residue: 0.9273 time to fit residues: 114.0169 Evaluate side-chains 118 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.0060 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4959 Z= 0.222 Angle : 0.698 11.046 6751 Z= 0.338 Chirality : 0.046 0.175 741 Planarity : 0.004 0.047 873 Dihedral : 4.744 26.321 684 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 4.82 % Allowed : 20.59 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.33), residues: 616 helix: -3.29 (0.75), residues: 34 sheet: 0.10 (0.36), residues: 219 loop : -2.92 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS A 519 PHE 0.018 0.001 PHE A 456 TYR 0.013 0.001 TYR L 174 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.570 Fit side-chains REVERT: H 58 THR cc_start: 0.8383 (p) cc_final: 0.8120 (p) REVERT: H 81 MET cc_start: 0.8238 (ttp) cc_final: 0.7946 (ttt) REVERT: H 132 LEU cc_start: 0.7074 (tm) cc_final: 0.6850 (tt) REVERT: L 6 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: L 10 THR cc_start: 0.8243 (p) cc_final: 0.7833 (m) REVERT: L 105 VAL cc_start: 0.8104 (t) cc_final: 0.7889 (m) REVERT: L 108 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7907 (mtpp) REVERT: L 127 LYS cc_start: 0.8902 (mttt) cc_final: 0.8592 (mttt) REVERT: L 147 VAL cc_start: 0.9185 (m) cc_final: 0.8906 (p) REVERT: L 175 SER cc_start: 0.8291 (t) cc_final: 0.7802 (p) REVERT: L 209 SER cc_start: 0.7636 (p) cc_final: 0.7343 (t) REVERT: A 358 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 386 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6262 (pttt) outliers start: 26 outliers final: 16 residues processed: 123 average time/residue: 0.8198 time to fit residues: 106.6241 Evaluate side-chains 119 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 56 optimal weight: 0.0070 chunk 6 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4959 Z= 0.287 Angle : 0.743 11.287 6751 Z= 0.365 Chirality : 0.047 0.199 741 Planarity : 0.005 0.050 873 Dihedral : 5.087 26.244 684 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 5.01 % Allowed : 20.78 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.33), residues: 616 helix: -3.23 (0.76), residues: 34 sheet: 0.19 (0.36), residues: 221 loop : -2.92 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 353 HIS 0.003 0.001 HIS A 519 PHE 0.017 0.002 PHE L 210 TYR 0.017 0.002 TYR L 174 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.569 Fit side-chains REVERT: H 132 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6852 (tt) REVERT: L 6 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: L 10 THR cc_start: 0.8230 (p) cc_final: 0.7854 (m) REVERT: L 20 THR cc_start: 0.8859 (p) cc_final: 0.8593 (p) REVERT: L 105 VAL cc_start: 0.8129 (t) cc_final: 0.7910 (m) REVERT: L 127 LYS cc_start: 0.8922 (mttt) cc_final: 0.8585 (mttt) REVERT: L 147 VAL cc_start: 0.9194 (m) cc_final: 0.8907 (p) REVERT: L 175 SER cc_start: 0.8271 (t) cc_final: 0.7816 (p) REVERT: L 209 SER cc_start: 0.7693 (p) cc_final: 0.7447 (t) REVERT: A 358 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7674 (mp) REVERT: A 386 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6319 (pttt) outliers start: 27 outliers final: 18 residues processed: 116 average time/residue: 0.8875 time to fit residues: 109.6579 Evaluate side-chains 119 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 0.0000 chunk 35 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4959 Z= 0.218 Angle : 0.719 11.625 6751 Z= 0.349 Chirality : 0.046 0.173 741 Planarity : 0.004 0.050 873 Dihedral : 4.903 26.028 684 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 4.27 % Allowed : 22.08 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.33), residues: 616 helix: -3.28 (0.77), residues: 34 sheet: 0.21 (0.36), residues: 221 loop : -2.88 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS A 519 PHE 0.015 0.001 PHE L 210 TYR 0.013 0.001 TYR L 174 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.651 Fit side-chains REVERT: H 81 MET cc_start: 0.8235 (ttp) cc_final: 0.7923 (ttt) REVERT: H 132 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6763 (tt) REVERT: L 6 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: L 10 THR cc_start: 0.8240 (p) cc_final: 0.7823 (m) REVERT: L 20 THR cc_start: 0.8820 (p) cc_final: 0.8519 (p) REVERT: L 105 VAL cc_start: 0.8227 (t) cc_final: 0.7981 (m) REVERT: L 108 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7913 (mtpp) REVERT: L 127 LYS cc_start: 0.8920 (mttt) cc_final: 0.8585 (mttt) REVERT: L 147 VAL cc_start: 0.9196 (m) cc_final: 0.8886 (p) REVERT: L 148 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7502 (tm-30) REVERT: L 175 SER cc_start: 0.8269 (t) cc_final: 0.7798 (p) REVERT: L 209 SER cc_start: 0.7659 (p) cc_final: 0.7458 (t) REVERT: A 358 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7569 (mp) outliers start: 23 outliers final: 18 residues processed: 115 average time/residue: 0.8681 time to fit residues: 105.2925 Evaluate side-chains 122 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 46 optimal weight: 0.4980 chunk 53 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4959 Z= 0.203 Angle : 0.722 11.681 6751 Z= 0.342 Chirality : 0.046 0.161 741 Planarity : 0.004 0.048 873 Dihedral : 4.796 25.545 684 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 4.08 % Allowed : 22.08 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.33), residues: 616 helix: -3.23 (0.76), residues: 34 sheet: 0.27 (0.36), residues: 221 loop : -2.78 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS A 519 PHE 0.015 0.001 PHE L 210 TYR 0.012 0.001 TYR A 501 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: H 81 MET cc_start: 0.8274 (ttp) cc_final: 0.7929 (ttt) REVERT: H 132 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6793 (tt) REVERT: L 10 THR cc_start: 0.8199 (p) cc_final: 0.7840 (m) REVERT: L 105 VAL cc_start: 0.8193 (t) cc_final: 0.7966 (m) REVERT: L 108 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7947 (mtpp) REVERT: L 127 LYS cc_start: 0.8928 (mttt) cc_final: 0.8593 (mttt) REVERT: L 147 VAL cc_start: 0.9177 (m) cc_final: 0.8916 (p) REVERT: L 148 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7406 (tm-30) REVERT: L 175 SER cc_start: 0.8305 (t) cc_final: 0.7840 (p) REVERT: A 386 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6309 (pttt) outliers start: 22 outliers final: 18 residues processed: 118 average time/residue: 0.8485 time to fit residues: 106.5408 Evaluate side-chains 120 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.0670 chunk 57 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4959 Z= 0.172 Angle : 0.701 11.747 6751 Z= 0.329 Chirality : 0.045 0.143 741 Planarity : 0.004 0.049 873 Dihedral : 4.610 25.193 684 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.71 % Allowed : 23.01 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.33), residues: 616 helix: -3.03 (0.80), residues: 34 sheet: 0.24 (0.36), residues: 223 loop : -2.64 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS A 519 PHE 0.014 0.001 PHE L 210 TYR 0.015 0.001 TYR A 501 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.526 Fit side-chains REVERT: H 81 MET cc_start: 0.8304 (ttp) cc_final: 0.8015 (ttt) REVERT: H 132 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6678 (tt) REVERT: L 10 THR cc_start: 0.8138 (p) cc_final: 0.7797 (m) REVERT: L 20 THR cc_start: 0.8798 (p) cc_final: 0.8366 (p) REVERT: L 101 GLN cc_start: 0.7039 (mp10) cc_final: 0.6728 (mp10) REVERT: L 108 LYS cc_start: 0.8289 (ttpp) cc_final: 0.7976 (mtpp) REVERT: L 127 LYS cc_start: 0.8901 (mttt) cc_final: 0.8586 (mttt) REVERT: A 386 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6284 (pttt) outliers start: 20 outliers final: 17 residues processed: 116 average time/residue: 0.8778 time to fit residues: 107.4179 Evaluate side-chains 119 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4959 Z= 0.240 Angle : 0.760 11.273 6751 Z= 0.361 Chirality : 0.047 0.172 741 Planarity : 0.005 0.052 873 Dihedral : 4.905 26.338 684 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 3.71 % Allowed : 24.49 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.33), residues: 616 helix: -3.08 (0.80), residues: 34 sheet: 0.11 (0.35), residues: 239 loop : -2.77 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS A 519 PHE 0.017 0.001 PHE L 210 TYR 0.015 0.002 TYR A 501 ARG 0.003 0.000 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.484 Fit side-chains REVERT: H 81 MET cc_start: 0.8297 (ttp) cc_final: 0.8017 (ttt) REVERT: H 132 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6872 (tt) REVERT: L 10 THR cc_start: 0.8186 (p) cc_final: 0.7833 (m) REVERT: L 20 THR cc_start: 0.8844 (p) cc_final: 0.8431 (p) REVERT: L 101 GLN cc_start: 0.7060 (mp10) cc_final: 0.6721 (mp10) REVERT: L 108 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7944 (mtpp) REVERT: L 127 LYS cc_start: 0.8912 (mttt) cc_final: 0.8592 (mttt) REVERT: L 175 SER cc_start: 0.8293 (t) cc_final: 0.7821 (p) REVERT: A 386 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6308 (pttt) outliers start: 20 outliers final: 18 residues processed: 109 average time/residue: 0.8967 time to fit residues: 103.1289 Evaluate side-chains 116 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 2 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 43 GLN A 409 GLN A 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127468 restraints weight = 7466.627| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.72 r_work: 0.3632 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4959 Z= 0.278 Angle : 0.783 11.275 6751 Z= 0.378 Chirality : 0.047 0.184 741 Planarity : 0.005 0.052 873 Dihedral : 5.134 27.352 684 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 4.27 % Allowed : 24.30 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.33), residues: 616 helix: -3.10 (0.79), residues: 34 sheet: 0.09 (0.35), residues: 239 loop : -2.84 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.000 HIS A 519 PHE 0.016 0.002 PHE L 210 TYR 0.016 0.002 TYR L 174 ARG 0.003 0.000 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.76 seconds wall clock time: 46 minutes 17.15 seconds (2777.15 seconds total)