Starting phenix.real_space_refine on Mon Dec 30 17:12:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7txt_26160/12_2024/7txt_26160_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7txt_26160/12_2024/7txt_26160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7txt_26160/12_2024/7txt_26160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7txt_26160/12_2024/7txt_26160.map" model { file = "/net/cci-nas-00/data/ceres_data/7txt_26160/12_2024/7txt_26160_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7txt_26160/12_2024/7txt_26160_trim.cif" } resolution = 3.0 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 Anisotropic ADP refinement not supported. Converting 1855 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 35 5.16 5 C 4011 2.51 5 N 967 2.21 5 O 1079 1.98 5 F 1 1.80 5 H 6018 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12111 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1824 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1651 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "S" Number of atoms: 8618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 8618 Classifications: {'peptide': 541} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'KWC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.07, per 1000 atoms: 0.58 Number of scatterers: 12111 At special positions: 0 Unit cell: (79.38, 72.09, 119.88, 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) S 35 16.00 F 1 9.00 O 1079 8.00 N 967 7.00 C 4011 6.00 H 6018 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 115 " distance=2.03 Simple disulfide: pdb=" SG CYS S 200 " - pdb=" SG CYS S 209 " 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: 3.18 Conformation dependent library (CDL) restraints added in 1.0 seconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 58.7% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.806A pdb=" N SER C 51 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.840A pdb=" N THR D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 97 Processing helix chain 'S' and resid 98 through 112 removed outlier: 3.965A pdb=" N VAL S 102 " --> pdb=" O ASP S 98 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE S 105 " --> pdb=" O ASN S 101 " (cutoff:3.500A) Proline residue: S 106 - end of helix Processing helix chain 'S' and resid 113 through 116 Processing helix chain 'S' and resid 117 through 127 Processing helix chain 'S' and resid 128 through 144 Processing helix chain 'S' and resid 148 through 153 removed outlier: 3.632A pdb=" N TRP S 151 " --> pdb=" O ILE S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 155 through 158 Processing helix chain 'S' and resid 159 through 190 removed outlier: 3.868A pdb=" N TYR S 163 " --> pdb=" O LYS S 159 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN S 177 " --> pdb=" O ALA S 173 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR S 178 " --> pdb=" O SER S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 235 Processing helix chain 'S' and resid 238 through 242 Processing helix chain 'S' and resid 252 through 270 Processing helix chain 'S' and resid 273 through 285 removed outlier: 4.632A pdb=" N LYS S 279 " --> pdb=" O LYS S 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP S 282 " --> pdb=" O GLY S 278 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL S 283 " --> pdb=" O LYS S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 302 Processing helix chain 'S' and resid 304 through 314 removed outlier: 3.671A pdb=" N GLY S 308 " --> pdb=" O GLY S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 316 through 321 Processing helix chain 'S' and resid 322 through 338 removed outlier: 4.154A pdb=" N TRP S 326 " --> pdb=" O GLU S 322 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 350 removed outlier: 3.777A pdb=" N TYR S 350 " --> pdb=" O ALA S 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 390 removed outlier: 3.615A pdb=" N VAL S 382 " --> pdb=" O VAL S 378 " (cutoff:3.500A) Processing helix chain 'S' and resid 393 through 399 Processing helix chain 'S' and resid 408 through 417 Processing helix chain 'S' and resid 419 through 454 removed outlier: 3.804A pdb=" N SER S 438 " --> pdb=" O LEU S 434 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL S 446 " --> pdb=" O GLY S 442 " (cutoff:3.500A) Processing helix chain 'S' and resid 454 through 459 Processing helix chain 'S' and resid 461 through 478 removed outlier: 3.566A pdb=" N PHE S 465 " --> pdb=" O ARG S 461 " (cutoff:3.500A) Processing helix chain 'S' and resid 479 through 482 Processing helix chain 'S' and resid 484 through 496 Processing helix chain 'S' and resid 498 through 514 removed outlier: 3.797A pdb=" N LEU S 502 " --> pdb=" O GLY S 498 " (cutoff:3.500A) Processing helix chain 'S' and resid 517 through 530 Processing helix chain 'S' and resid 534 through 543 Processing helix chain 'S' and resid 543 through 558 Processing helix chain 'S' and resid 571 through 587 Processing helix chain 'S' and resid 587 through 600 Processing helix chain 'S' and resid 603 through 613 removed outlier: 4.192A pdb=" N SER S 611 " --> pdb=" O ARG S 607 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.321A pdb=" N MET C 53 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG C 69 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP C 55 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 24 through 27 removed outlier: 3.577A pdb=" N TYR D 94 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 30 through 34 removed outlier: 6.397A pdb=" N LEU D 31 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS D 131 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 33 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TRP D 59 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 564 through 565 removed outlier: 3.594A pdb=" N LEU S 565 " --> pdb=" O TYR S 568 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1008 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: 4.80 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5999 1.03 - 1.23: 32 1.23 - 1.42: 2745 1.42 - 1.62: 3468 1.62 - 1.81: 49 Bond restraints: 12293 Sorted by residual: bond pdb=" CAI KWC S 701 " pdb=" SAH KWC S 701 " ideal model delta sigma weight residual 1.750 1.458 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" CAB KWC S 701 " pdb=" FAA KWC S 701 " ideal model delta sigma weight residual 1.342 1.096 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" CAE KWC S 701 " pdb=" CAF KWC S 701 " ideal model delta sigma weight residual 1.470 1.308 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" CAG KWC S 701 " pdb=" SAH KWC S 701 " ideal model delta sigma weight residual 1.725 1.573 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CAK KWC S 701 " pdb=" CAL KWC S 701 " ideal model delta sigma weight residual 1.524 1.473 0.051 2.00e-02 2.50e+03 6.57e+00 ... (remaining 12288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.11: 22120 6.11 - 12.21: 1 12.21 - 18.32: 0 18.32 - 24.42: 2 24.42 - 30.53: 4 Bond angle restraints: 22127 Sorted by residual: angle pdb=" HB2 ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB3 ALA S 401 " ideal model delta sigma weight residual 110.00 79.47 30.53 3.00e+00 1.11e-01 1.04e+02 angle pdb=" HB1 ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB2 ALA S 401 " ideal model delta sigma weight residual 110.00 80.41 29.59 3.00e+00 1.11e-01 9.73e+01 angle pdb=" CA ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB3 ALA S 401 " ideal model delta sigma weight residual 109.00 79.72 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CA ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB1 ALA S 401 " ideal model delta sigma weight residual 109.00 81.70 27.30 3.00e+00 1.11e-01 8.28e+01 angle pdb=" CA ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB2 ALA S 401 " ideal model delta sigma weight residual 109.00 131.86 -22.86 3.00e+00 1.11e-01 5.81e+01 ... (remaining 22122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5355 17.77 - 35.54: 327 35.54 - 53.30: 127 53.30 - 71.07: 36 71.07 - 88.84: 9 Dihedral angle restraints: 5854 sinusoidal: 3033 harmonic: 2821 Sorted by residual: dihedral pdb=" CB CYS C 41 " pdb=" SG CYS C 41 " pdb=" SG CYS C 115 " pdb=" CB CYS C 115 " ideal model delta sinusoidal sigma weight residual 93.00 59.30 33.70 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CA GLY S 402 " pdb=" C GLY S 402 " pdb=" N PRO S 403 " pdb=" CA PRO S 403 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ALA S 459 " pdb=" C ALA S 459 " pdb=" N LYS S 460 " pdb=" CA LYS S 460 " ideal model delta harmonic sigma weight residual 180.00 164.38 15.62 0 5.00e+00 4.00e-02 9.76e+00 ... (remaining 5851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 687 0.037 - 0.074: 188 0.074 - 0.112: 52 0.112 - 0.149: 10 0.149 - 0.186: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA ILE D 72 " pdb=" N ILE D 72 " pdb=" C ILE D 72 " pdb=" CB ILE D 72 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CA ILE D 41 " pdb=" N ILE D 41 " pdb=" C ILE D 41 " pdb=" CB ILE D 41 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE D 99 " pdb=" N ILE D 99 " pdb=" C ILE D 99 " pdb=" CB ILE D 99 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 935 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 271 " 0.015 2.00e-02 2.50e+03 1.01e-02 4.06e+00 pdb=" CG TRP S 271 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP S 271 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP S 271 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP S 271 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP S 271 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 271 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 271 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 271 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP S 271 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP S 271 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP S 271 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP S 271 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP S 271 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP S 271 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP S 271 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE S 130 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO S 131 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO S 131 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 131 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS S 155 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO S 156 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO S 156 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 156 " 0.022 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 521 2.16 - 2.77: 23836 2.77 - 3.38: 37044 3.38 - 3.99: 48147 3.99 - 4.60: 75936 Nonbonded interactions: 185484 Sorted by model distance: nonbonded pdb=" HE ARG C 38 " pdb=" OE1 GLN C 101 " model vdw 1.544 2.450 nonbonded pdb=" OE2 GLU S 444 " pdb=" HG1 THR S 448 " model vdw 1.637 2.450 nonbonded pdb=" O CYS S 109 " pdb=" H GLY S 114 " model vdw 1.645 2.450 nonbonded pdb=" O VAL S 367 " pdb=" HG1 THR S 371 " model vdw 1.649 2.450 nonbonded pdb=" O TRP S 204 " pdb="HH11 ARG S 234 " model vdw 1.659 2.450 ... (remaining 185479 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.210 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.007 0.292 6275 Z= 0.482 Angle : 0.530 11.580 8543 Z= 0.285 Chirality : 0.039 0.186 938 Planarity : 0.004 0.047 1053 Dihedral : 12.667 88.841 2166 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.25 (0.31), residues: 766 helix: 0.70 (0.26), residues: 387 sheet: -0.54 (0.45), residues: 125 loop : -0.05 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP S 271 HIS 0.003 0.001 HIS S 143 PHE 0.016 0.001 PHE S 548 TYR 0.017 0.001 TYR D 73 ARG 0.007 0.000 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.886 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 2.6822 time to fit residues: 346.0036 Evaluate side-chains 97 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.0020 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 69 optimal weight: 0.0170 overall best weight: 0.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN S 391 ASN S 416 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6275 Z= 0.196 Angle : 0.538 5.204 8543 Z= 0.293 Chirality : 0.040 0.166 938 Planarity : 0.005 0.049 1053 Dihedral : 4.212 20.709 849 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.24 % Allowed : 8.67 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.53 (0.31), residues: 766 helix: 0.99 (0.26), residues: 389 sheet: -0.35 (0.46), residues: 123 loop : -0.09 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 103 HIS 0.002 0.001 HIS S 143 PHE 0.018 0.001 PHE S 548 TYR 0.021 0.001 TYR D 73 ARG 0.006 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 ASP cc_start: 0.8190 (m-30) cc_final: 0.7979 (m-30) REVERT: D 104 GLU cc_start: 0.7195 (tp30) cc_final: 0.6932 (tp30) outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 2.3895 time to fit residues: 252.3452 Evaluate side-chains 95 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain S residue 327 ILE Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6275 Z= 0.251 Angle : 0.516 4.876 8543 Z= 0.282 Chirality : 0.039 0.160 938 Planarity : 0.005 0.055 1053 Dihedral : 4.028 15.980 849 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.24 % Allowed : 9.13 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.48 (0.30), residues: 766 helix: 0.99 (0.26), residues: 389 sheet: -0.27 (0.47), residues: 121 loop : -0.24 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.019 0.001 PHE S 548 TYR 0.024 0.001 TYR D 73 ARG 0.004 0.000 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 109 ASP cc_start: 0.8190 (m-30) cc_final: 0.7965 (m-30) REVERT: D 104 GLU cc_start: 0.7212 (tp30) cc_final: 0.6954 (tp30) outliers start: 8 outliers final: 4 residues processed: 97 average time/residue: 2.4846 time to fit residues: 254.9487 Evaluate side-chains 92 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6275 Z= 0.268 Angle : 0.513 5.002 8543 Z= 0.280 Chirality : 0.039 0.160 938 Planarity : 0.005 0.059 1053 Dihedral : 3.969 15.841 849 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.77 % Allowed : 10.06 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.44 (0.30), residues: 766 helix: 0.98 (0.26), residues: 390 sheet: -0.30 (0.47), residues: 121 loop : -0.30 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.019 0.001 PHE S 548 TYR 0.023 0.001 TYR D 73 ARG 0.007 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: D 127 LYS cc_start: 0.8396 (tttp) cc_final: 0.8190 (tptm) outliers start: 5 outliers final: 4 residues processed: 96 average time/residue: 2.4235 time to fit residues: 245.5458 Evaluate side-chains 92 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6275 Z= 0.260 Angle : 0.514 5.135 8543 Z= 0.279 Chirality : 0.039 0.158 938 Planarity : 0.005 0.061 1053 Dihedral : 3.955 15.449 849 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.39 % Allowed : 10.22 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.42 (0.30), residues: 766 helix: 1.01 (0.26), residues: 391 sheet: -0.36 (0.47), residues: 121 loop : -0.35 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.022 0.001 TYR D 73 ARG 0.007 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 127 LYS cc_start: 0.8386 (tttp) cc_final: 0.8185 (tptm) outliers start: 9 outliers final: 3 residues processed: 99 average time/residue: 2.4831 time to fit residues: 259.1189 Evaluate side-chains 89 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6275 Z= 0.243 Angle : 0.513 5.250 8543 Z= 0.279 Chirality : 0.039 0.160 938 Planarity : 0.005 0.066 1053 Dihedral : 3.939 15.383 849 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.08 % Allowed : 11.46 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.41 (0.30), residues: 766 helix: 1.05 (0.26), residues: 391 sheet: -0.43 (0.47), residues: 121 loop : -0.42 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.016 0.001 PHE S 548 TYR 0.022 0.001 TYR D 73 ARG 0.008 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: C 47 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7409 (ptm-80) REVERT: D 127 LYS cc_start: 0.8370 (tttp) cc_final: 0.8167 (tptm) outliers start: 7 outliers final: 3 residues processed: 97 average time/residue: 2.3591 time to fit residues: 242.2910 Evaluate side-chains 93 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6275 Z= 0.268 Angle : 0.518 5.477 8543 Z= 0.281 Chirality : 0.039 0.160 938 Planarity : 0.005 0.069 1053 Dihedral : 3.955 15.271 849 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.08 % Allowed : 12.07 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.47 (0.30), residues: 766 helix: 1.05 (0.26), residues: 392 sheet: -0.31 (0.47), residues: 118 loop : -0.38 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.022 0.001 TYR D 73 ARG 0.009 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.944 Fit side-chains REVERT: C 47 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7505 (ptm-80) REVERT: C 123 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7608 (mt-10) outliers start: 7 outliers final: 3 residues processed: 96 average time/residue: 2.3931 time to fit residues: 242.6472 Evaluate side-chains 94 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6275 Z= 0.236 Angle : 0.515 5.792 8543 Z= 0.279 Chirality : 0.039 0.160 938 Planarity : 0.005 0.071 1053 Dihedral : 3.938 15.452 849 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.93 % Allowed : 12.85 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.43 (0.30), residues: 766 helix: 1.01 (0.26), residues: 392 sheet: -0.33 (0.47), residues: 118 loop : -0.38 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.016 0.001 PHE S 548 TYR 0.022 0.001 TYR D 73 ARG 0.009 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.959 Fit side-chains REVERT: C 47 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7437 (ptm-80) REVERT: C 123 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7587 (mt-10) outliers start: 6 outliers final: 3 residues processed: 97 average time/residue: 2.3879 time to fit residues: 244.5997 Evaluate side-chains 93 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.0770 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6275 Z= 0.212 Angle : 0.506 5.257 8543 Z= 0.275 Chirality : 0.039 0.163 938 Planarity : 0.005 0.076 1053 Dihedral : 3.905 15.638 849 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.62 % Allowed : 12.85 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.52 (0.30), residues: 766 helix: 1.07 (0.26), residues: 392 sheet: -0.30 (0.47), residues: 118 loop : -0.30 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 103 HIS 0.002 0.001 HIS S 143 PHE 0.015 0.001 PHE S 548 TYR 0.023 0.001 TYR D 73 ARG 0.010 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.933 Fit side-chains REVERT: C 47 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7447 (ptm-80) outliers start: 4 outliers final: 3 residues processed: 100 average time/residue: 2.4175 time to fit residues: 255.7740 Evaluate side-chains 97 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 111 GLN ** S 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6275 Z= 0.260 Angle : 0.534 5.626 8543 Z= 0.292 Chirality : 0.039 0.161 938 Planarity : 0.005 0.077 1053 Dihedral : 3.942 15.315 849 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.93 % Allowed : 13.16 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.51 (0.30), residues: 766 helix: 1.09 (0.26), residues: 392 sheet: -0.31 (0.47), residues: 118 loop : -0.34 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 103 HIS 0.003 0.001 HIS S 223 PHE 0.017 0.001 PHE S 548 TYR 0.022 0.001 TYR D 73 ARG 0.011 0.001 ARG S 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 1.003 Fit side-chains REVERT: C 47 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7528 (ptm-80) REVERT: C 123 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7594 (mt-10) outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 2.4337 time to fit residues: 243.9900 Evaluate side-chains 96 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.086143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.074066 restraints weight = 30949.176| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.11 r_work: 0.2703 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6275 Z= 0.212 Angle : 0.523 6.769 8543 Z= 0.286 Chirality : 0.039 0.162 938 Planarity : 0.005 0.076 1053 Dihedral : 3.929 15.332 849 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.77 % Allowed : 13.16 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.60 (0.30), residues: 766 helix: 1.13 (0.26), residues: 392 sheet: -0.26 (0.47), residues: 118 loop : -0.27 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 103 HIS 0.003 0.001 HIS S 223 PHE 0.015 0.001 PHE S 548 TYR 0.023 0.001 TYR D 73 ARG 0.011 0.001 ARG S 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5433.23 seconds wall clock time: 96 minutes 53.72 seconds (5813.72 seconds total)