Starting phenix.real_space_refine on Wed Jan 17 17:26:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/01_2024/6zqi_11364.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/01_2024/6zqi_11364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/01_2024/6zqi_11364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/01_2024/6zqi_11364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/01_2024/6zqi_11364.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/01_2024/6zqi_11364.pdb" } resolution = 3.8 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= 0.005 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 43 5.16 5 C 3167 2.51 5 N 875 2.21 5 O 947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "B" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.51, per 1000 atoms: 0.70 Number of scatterers: 5032 At special positions: 0 Unit cell: (74.36, 123.37, 138.58, 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 43 16.00 O 947 8.00 N 875 7.00 C 3167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 69 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 81 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 67 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG B 201 " - " ASN B 70 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 963.9 milliseconds 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1182 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 23.4% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.808A pdb=" N ALA A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.603A pdb=" N HIS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 220' Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.598A pdb=" N THR A 395 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 396 " --> pdb=" O GLY A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 396' Processing helix chain 'A' and resid 406 through 425 Processing helix chain 'A' and resid 437 through 458 removed outlier: 5.797A pdb=" N SER A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.538A pdb=" N LEU A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 502 removed outlier: 3.726A pdb=" N PHE A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.026A pdb=" N THR C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 7.173A pdb=" N ARG A 138 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.690A pdb=" N GLU A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.926A pdb=" N LYS A 291 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 removed outlier: 7.034A pdb=" N GLY A 127 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER A 58 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 125 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N CYS A 60 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS A 123 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 62 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N CYS A 121 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 274 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 73 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 6.641A pdb=" N ALA A 307 " --> pdb=" O LYS A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.568A pdb=" N SER A 320 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.965A pdb=" N ARG A 358 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 347 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.199A pdb=" N TYR B 10 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 77 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N MET B 12 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY B 79 " --> pdb=" O MET B 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 26 213 hydrogen bonds defined for protein. 576 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: 1.51 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1646 1.35 - 1.47: 1271 1.47 - 1.59: 2159 1.59 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 5144 Sorted by residual: bond pdb=" N ARG B 94 " pdb=" CA ARG B 94 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.30e+00 bond pdb=" N HIS A 250 " pdb=" CA HIS A 250 " ideal model delta sigma weight residual 1.455 1.482 -0.028 1.25e-02 6.40e+03 4.94e+00 bond pdb=" N HIS B 101 " pdb=" CA HIS B 101 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" CE1 HIS A 250 " pdb=" NE2 HIS A 250 " ideal model delta sigma weight residual 1.321 1.336 -0.015 1.00e-02 1.00e+04 2.22e+00 bond pdb=" CE1 HIS B 101 " pdb=" NE2 HIS B 101 " ideal model delta sigma weight residual 1.321 1.336 -0.015 1.00e-02 1.00e+04 2.19e+00 ... (remaining 5139 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.04: 144 107.04 - 113.78: 2891 113.78 - 120.51: 1839 120.51 - 127.24: 2019 127.24 - 133.98: 69 Bond angle restraints: 6962 Sorted by residual: angle pdb=" CA CYS A 116 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " ideal model delta sigma weight residual 114.40 126.73 -12.33 2.30e+00 1.89e-01 2.87e+01 angle pdb=" CA CYS A 92 " pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " ideal model delta sigma weight residual 114.40 125.70 -11.30 2.30e+00 1.89e-01 2.41e+01 angle pdb=" N CYS A 116 " pdb=" CA CYS A 116 " pdb=" C CYS A 116 " ideal model delta sigma weight residual 109.52 114.59 -5.07 1.55e+00 4.16e-01 1.07e+01 angle pdb=" C SER B 71 " pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 122.32 127.75 -5.43 1.76e+00 3.23e-01 9.52e+00 angle pdb=" C LYS A 444 " pdb=" N PHE A 445 " pdb=" CA PHE A 445 " ideal model delta sigma weight residual 120.68 116.13 4.55 1.70e+00 3.46e-01 7.16e+00 ... (remaining 6957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2817 17.87 - 35.75: 189 35.75 - 53.62: 39 53.62 - 71.50: 6 71.50 - 89.37: 5 Dihedral angle restraints: 3056 sinusoidal: 1203 harmonic: 1853 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual 93.00 -179.58 -87.42 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual -86.00 -23.78 -62.22 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS B 34 " pdb=" SG CYS B 34 " pdb=" SG CYS B 69 " pdb=" CB CYS B 69 " ideal model delta sinusoidal sigma weight residual -86.00 -28.93 -57.07 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 3053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 602 0.048 - 0.097: 137 0.097 - 0.145: 30 0.145 - 0.193: 3 0.193 - 0.241: 1 Chirality restraints: 773 Sorted by residual: chirality pdb=" CA CYS A 116 " pdb=" N CYS A 116 " pdb=" C CYS A 116 " pdb=" CB CYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA CYS A 92 " pdb=" N CYS A 92 " pdb=" C CYS A 92 " pdb=" CB CYS A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ARG B 94 " pdb=" N ARG B 94 " pdb=" C ARG B 94 " pdb=" CB ARG B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 770 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 74 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO A 75 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 45 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 46 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 53 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO B 54 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.014 5.00e-02 4.00e+02 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1744 2.85 - 3.36: 4336 3.36 - 3.87: 7621 3.87 - 4.39: 8126 4.39 - 4.90: 14511 Nonbonded interactions: 36338 Sorted by model distance: nonbonded pdb=" OD1 ASP A 380 " pdb=" NH1 ARG A 403 " model vdw 2.336 2.520 nonbonded pdb=" OG1 THR A 322 " pdb=" OG1 THR A 326 " model vdw 2.361 2.440 nonbonded pdb=" O ILE A 497 " pdb=" OG1 THR A 501 " model vdw 2.370 2.440 nonbonded pdb=" OE1 GLU A 178 " pdb=" OG SER A 188 " model vdw 2.385 2.440 nonbonded pdb=" O SER A 369 " pdb=" OG SER A 369 " model vdw 2.389 2.440 ... (remaining 36333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.330 Find NCS groups from input model: 0.130 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 0.031 5144 Z= 0.163 Angle : 0.565 12.331 6962 Z= 0.325 Chirality : 0.044 0.241 773 Planarity : 0.003 0.032 887 Dihedral : 12.439 89.370 1847 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.12 % Allowed : 3.72 % Favored : 95.16 % 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: -2.14 (0.29), residues: 649 helix: -0.02 (0.42), residues: 132 sheet: -0.56 (0.35), residues: 197 loop : -2.67 (0.27), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.002 0.000 HIS A 160 PHE 0.017 0.001 PHE A 445 TYR 0.010 0.001 TYR A 61 ARG 0.003 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 189 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7547 (mtm) cc_final: 0.7152 (mtm) REVERT: A 77 GLN cc_start: 0.8105 (tp40) cc_final: 0.7776 (mt0) REVERT: A 81 TYR cc_start: 0.8482 (t80) cc_final: 0.8174 (t80) REVERT: A 178 GLU cc_start: 0.7788 (tp30) cc_final: 0.7464 (mm-30) REVERT: A 201 ASP cc_start: 0.8099 (t0) cc_final: 0.7829 (t0) REVERT: A 209 ASN cc_start: 0.8389 (t0) cc_final: 0.8050 (t0) REVERT: A 221 ASP cc_start: 0.7948 (t70) cc_final: 0.7688 (t0) REVERT: A 330 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7131 (mt-10) REVERT: A 374 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8178 (mmtm) REVERT: A 422 MET cc_start: 0.8617 (tpp) cc_final: 0.8021 (tpp) REVERT: A 432 PHE cc_start: 0.7640 (m-10) cc_final: 0.4941 (p90) REVERT: A 447 HIS cc_start: 0.8448 (t-90) cc_final: 0.7942 (t-170) REVERT: A 455 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7000 (mptt) REVERT: A 471 PHE cc_start: 0.8609 (m-10) cc_final: 0.7968 (t80) REVERT: B 32 ASN cc_start: 0.6953 (t0) cc_final: 0.6699 (t0) REVERT: B 39 MET cc_start: 0.7032 (ptt) cc_final: 0.6826 (ttt) REVERT: B 101 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7546 (m-70) REVERT: C 127 GLU cc_start: 0.8549 (tt0) cc_final: 0.8067 (mt-10) outliers start: 6 outliers final: 1 residues processed: 192 average time/residue: 0.1970 time to fit residues: 46.4336 Evaluate side-chains 150 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain B residue 101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 363 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5144 Z= 0.211 Angle : 0.622 15.154 6962 Z= 0.320 Chirality : 0.045 0.284 773 Planarity : 0.004 0.034 887 Dihedral : 5.744 78.462 726 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.28 % Allowed : 14.53 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.31), residues: 649 helix: 1.33 (0.46), residues: 131 sheet: -0.25 (0.36), residues: 195 loop : -2.20 (0.29), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.009 0.001 PHE A 445 TYR 0.012 0.001 TYR A 61 ARG 0.005 0.001 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8246 (tp40) cc_final: 0.8033 (mt0) REVERT: A 81 TYR cc_start: 0.8569 (t80) cc_final: 0.8178 (t80) REVERT: A 178 GLU cc_start: 0.7927 (tp30) cc_final: 0.7543 (mm-30) REVERT: A 201 ASP cc_start: 0.8172 (t0) cc_final: 0.7906 (t0) REVERT: A 203 TYR cc_start: 0.8363 (m-10) cc_final: 0.7936 (m-80) REVERT: A 221 ASP cc_start: 0.8094 (t70) cc_final: 0.7811 (t0) REVERT: A 365 VAL cc_start: 0.9122 (p) cc_final: 0.8871 (p) REVERT: A 422 MET cc_start: 0.8669 (tpp) cc_final: 0.8043 (tpp) REVERT: A 432 PHE cc_start: 0.7700 (m-10) cc_final: 0.4961 (p90) REVERT: A 447 HIS cc_start: 0.8559 (t-90) cc_final: 0.8098 (t-170) REVERT: A 455 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7304 (mptt) REVERT: A 471 PHE cc_start: 0.8642 (m-10) cc_final: 0.7981 (t80) REVERT: B 32 ASN cc_start: 0.6817 (t0) cc_final: 0.6428 (t0) outliers start: 23 outliers final: 14 residues processed: 167 average time/residue: 0.1644 time to fit residues: 35.0781 Evaluate side-chains 162 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS B 59 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5144 Z= 0.297 Angle : 0.677 19.652 6962 Z= 0.349 Chirality : 0.047 0.331 773 Planarity : 0.004 0.039 887 Dihedral : 5.823 79.721 724 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.28 % Allowed : 21.97 % Favored : 73.74 % 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: -1.01 (0.32), residues: 649 helix: 1.58 (0.46), residues: 132 sheet: -0.31 (0.35), residues: 202 loop : -1.96 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 129 HIS 0.006 0.001 HIS A 27 PHE 0.017 0.002 PHE A 458 TYR 0.018 0.002 TYR A 61 ARG 0.005 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8289 (t80) cc_final: 0.7900 (t80) REVERT: A 131 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7308 (mm110) REVERT: A 178 GLU cc_start: 0.7916 (tp30) cc_final: 0.7494 (mm-30) REVERT: A 201 ASP cc_start: 0.8202 (t0) cc_final: 0.7967 (t0) REVERT: A 221 ASP cc_start: 0.8171 (t70) cc_final: 0.7892 (t0) REVERT: A 332 GLN cc_start: 0.7152 (tt0) cc_final: 0.6767 (tm-30) REVERT: A 412 PHE cc_start: 0.7764 (t80) cc_final: 0.7558 (t80) REVERT: A 422 MET cc_start: 0.8644 (tpp) cc_final: 0.8069 (tpp) REVERT: A 438 MET cc_start: 0.6526 (mpp) cc_final: 0.6020 (mpp) REVERT: A 447 HIS cc_start: 0.8738 (t-90) cc_final: 0.8194 (t-170) REVERT: A 466 GLN cc_start: 0.8935 (mp10) cc_final: 0.8503 (pm20) REVERT: A 471 PHE cc_start: 0.8716 (m-10) cc_final: 0.8051 (t80) REVERT: B 32 ASN cc_start: 0.7028 (t0) cc_final: 0.6678 (t0) outliers start: 23 outliers final: 17 residues processed: 166 average time/residue: 0.1607 time to fit residues: 34.4367 Evaluate side-chains 160 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 0.0670 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5144 Z= 0.161 Angle : 0.595 13.504 6962 Z= 0.307 Chirality : 0.044 0.219 773 Planarity : 0.003 0.038 887 Dihedral : 5.505 80.756 724 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.10 % Allowed : 24.02 % Favored : 71.88 % 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: -0.64 (0.32), residues: 649 helix: 2.08 (0.48), residues: 131 sheet: -0.04 (0.37), residues: 191 loop : -1.79 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.025 0.001 PHE A 498 TYR 0.017 0.001 TYR A 203 ARG 0.003 0.000 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8692 (t80) cc_final: 0.8331 (t80) REVERT: A 178 GLU cc_start: 0.7822 (tp30) cc_final: 0.7421 (mm-30) REVERT: A 192 GLU cc_start: 0.7989 (mp0) cc_final: 0.7578 (mp0) REVERT: A 201 ASP cc_start: 0.8364 (t0) cc_final: 0.7972 (t0) REVERT: A 221 ASP cc_start: 0.8126 (t70) cc_final: 0.7858 (t0) REVERT: A 412 PHE cc_start: 0.7655 (t80) cc_final: 0.7423 (t80) REVERT: A 422 MET cc_start: 0.8533 (tpp) cc_final: 0.7919 (tpp) REVERT: A 438 MET cc_start: 0.6334 (mpp) cc_final: 0.5922 (mpp) REVERT: A 447 HIS cc_start: 0.8766 (t-90) cc_final: 0.8135 (t-170) REVERT: A 455 LYS cc_start: 0.7476 (ttmt) cc_final: 0.6955 (mptt) REVERT: A 466 GLN cc_start: 0.8982 (mp10) cc_final: 0.8176 (pm20) REVERT: A 471 PHE cc_start: 0.8696 (m-10) cc_final: 0.8022 (t80) REVERT: B 32 ASN cc_start: 0.6974 (t0) cc_final: 0.6643 (t0) outliers start: 22 outliers final: 14 residues processed: 164 average time/residue: 0.1586 time to fit residues: 33.7210 Evaluate side-chains 158 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5144 Z= 0.219 Angle : 0.635 21.348 6962 Z= 0.328 Chirality : 0.045 0.311 773 Planarity : 0.004 0.039 887 Dihedral : 5.491 81.015 724 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.47 % Allowed : 24.39 % Favored : 71.14 % 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: -0.55 (0.33), residues: 649 helix: 2.18 (0.47), residues: 131 sheet: -0.05 (0.37), residues: 192 loop : -1.71 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.028 0.002 PHE A 454 TYR 0.014 0.001 TYR A 61 ARG 0.003 0.000 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8307 (t80) cc_final: 0.7929 (t80) REVERT: A 178 GLU cc_start: 0.7803 (tp30) cc_final: 0.7405 (mm-30) REVERT: A 192 GLU cc_start: 0.8076 (mp0) cc_final: 0.7612 (mp0) REVERT: A 201 ASP cc_start: 0.8368 (t0) cc_final: 0.8050 (t0) REVERT: A 221 ASP cc_start: 0.8157 (t70) cc_final: 0.7869 (t0) REVERT: A 332 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7369 (tt0) REVERT: A 412 PHE cc_start: 0.7701 (t80) cc_final: 0.7463 (t80) REVERT: A 422 MET cc_start: 0.8490 (tpp) cc_final: 0.7971 (tpp) REVERT: A 438 MET cc_start: 0.6546 (mpp) cc_final: 0.6114 (mpp) REVERT: A 447 HIS cc_start: 0.8815 (t-90) cc_final: 0.8174 (t-170) REVERT: A 455 LYS cc_start: 0.7589 (ttmt) cc_final: 0.7089 (mptt) REVERT: A 471 PHE cc_start: 0.8739 (m-10) cc_final: 0.8063 (t80) REVERT: B 32 ASN cc_start: 0.6748 (t0) cc_final: 0.6544 (t0) REVERT: C 161 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7930 (mm) outliers start: 24 outliers final: 17 residues processed: 165 average time/residue: 0.1537 time to fit residues: 32.7622 Evaluate side-chains 156 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5144 Z= 0.181 Angle : 0.635 14.699 6962 Z= 0.324 Chirality : 0.045 0.247 773 Planarity : 0.003 0.039 887 Dihedral : 5.403 82.166 724 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.72 % Allowed : 26.63 % Favored : 69.65 % 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: -0.42 (0.33), residues: 649 helix: 2.28 (0.47), residues: 131 sheet: 0.11 (0.38), residues: 192 loop : -1.67 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.022 0.001 PHE A 454 TYR 0.021 0.001 TYR A 203 ARG 0.003 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8291 (t80) cc_final: 0.7819 (t80) REVERT: A 178 GLU cc_start: 0.7807 (tp30) cc_final: 0.7407 (mm-30) REVERT: A 192 GLU cc_start: 0.7978 (mp0) cc_final: 0.7473 (mp0) REVERT: A 201 ASP cc_start: 0.8402 (t0) cc_final: 0.7984 (t0) REVERT: A 221 ASP cc_start: 0.8148 (t70) cc_final: 0.7861 (t0) REVERT: A 332 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7712 (tt0) REVERT: A 412 PHE cc_start: 0.7686 (t80) cc_final: 0.7446 (t80) REVERT: A 422 MET cc_start: 0.8486 (tpp) cc_final: 0.7962 (tpp) REVERT: A 447 HIS cc_start: 0.8847 (t-90) cc_final: 0.8204 (t-170) REVERT: A 455 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7142 (mptt) REVERT: A 466 GLN cc_start: 0.8857 (mp10) cc_final: 0.8271 (pm20) REVERT: A 471 PHE cc_start: 0.8746 (m-10) cc_final: 0.8063 (t80) REVERT: B 6 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7159 (ptpp) REVERT: B 32 ASN cc_start: 0.6846 (t0) cc_final: 0.6508 (t0) REVERT: C 161 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8006 (mm) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.1466 time to fit residues: 29.8675 Evaluate side-chains 156 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5144 Z= 0.240 Angle : 0.691 23.116 6962 Z= 0.352 Chirality : 0.047 0.331 773 Planarity : 0.004 0.040 887 Dihedral : 5.587 82.292 724 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.03 % Allowed : 26.07 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.33), residues: 649 helix: 2.32 (0.46), residues: 131 sheet: 0.07 (0.38), residues: 187 loop : -1.64 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 129 HIS 0.006 0.001 HIS A 27 PHE 0.021 0.002 PHE A 498 TYR 0.023 0.002 TYR A 203 ARG 0.003 0.000 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8361 (t80) cc_final: 0.7754 (t80) REVERT: A 178 GLU cc_start: 0.7930 (tp30) cc_final: 0.7506 (mm-30) REVERT: A 192 GLU cc_start: 0.8055 (mp0) cc_final: 0.7566 (mp0) REVERT: A 201 ASP cc_start: 0.8721 (t0) cc_final: 0.8227 (t0) REVERT: A 221 ASP cc_start: 0.8188 (t70) cc_final: 0.7907 (t0) REVERT: A 412 PHE cc_start: 0.7728 (t80) cc_final: 0.7491 (t80) REVERT: A 422 MET cc_start: 0.8470 (tpp) cc_final: 0.7969 (tpp) REVERT: A 455 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7178 (mptt) REVERT: A 471 PHE cc_start: 0.8789 (m-10) cc_final: 0.8105 (t80) REVERT: B 34 CYS cc_start: 0.6510 (t) cc_final: 0.6075 (t) REVERT: C 161 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8039 (mm) outliers start: 27 outliers final: 20 residues processed: 158 average time/residue: 0.1566 time to fit residues: 32.4568 Evaluate side-chains 157 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 5144 Z= 0.325 Angle : 0.740 18.384 6962 Z= 0.380 Chirality : 0.048 0.316 773 Planarity : 0.004 0.041 887 Dihedral : 5.911 81.647 724 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.66 % Allowed : 27.56 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.64 (0.33), residues: 649 helix: 1.74 (0.45), residues: 136 sheet: -0.02 (0.38), residues: 197 loop : -1.73 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 129 HIS 0.009 0.001 HIS A 447 PHE 0.022 0.002 PHE A 498 TYR 0.020 0.002 TYR A 61 ARG 0.004 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 0.610 Fit side-chains REVERT: A 77 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8133 (mm-40) REVERT: A 81 TYR cc_start: 0.8438 (t80) cc_final: 0.8214 (t80) REVERT: A 178 GLU cc_start: 0.7852 (tp30) cc_final: 0.7360 (mm-30) REVERT: A 192 GLU cc_start: 0.8181 (mp0) cc_final: 0.7627 (mp0) REVERT: A 201 ASP cc_start: 0.8623 (t0) cc_final: 0.8150 (t0) REVERT: A 203 TYR cc_start: 0.8722 (m-80) cc_final: 0.8358 (m-80) REVERT: A 221 ASP cc_start: 0.8240 (t70) cc_final: 0.7954 (t0) REVERT: A 332 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7277 (tt0) REVERT: A 412 PHE cc_start: 0.7805 (t80) cc_final: 0.7578 (t80) REVERT: A 422 MET cc_start: 0.8645 (tpp) cc_final: 0.8203 (tpp) REVERT: A 455 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7193 (mptt) REVERT: A 471 PHE cc_start: 0.8890 (m-10) cc_final: 0.8095 (t80) REVERT: B 32 ASN cc_start: 0.6835 (t0) cc_final: 0.6479 (t0) REVERT: B 60 TYR cc_start: 0.8893 (m-80) cc_final: 0.8689 (m-80) REVERT: C 128 ASN cc_start: 0.8424 (t0) cc_final: 0.7850 (t0) REVERT: C 161 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7630 (mm) outliers start: 25 outliers final: 23 residues processed: 159 average time/residue: 0.1560 time to fit residues: 32.3598 Evaluate side-chains 160 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 5144 Z= 0.359 Angle : 0.774 20.629 6962 Z= 0.398 Chirality : 0.050 0.345 773 Planarity : 0.004 0.042 887 Dihedral : 6.051 80.579 724 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.40 % Allowed : 27.00 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.81 (0.33), residues: 649 helix: 1.58 (0.45), residues: 136 sheet: -0.16 (0.38), residues: 197 loop : -1.80 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 129 HIS 0.006 0.001 HIS A 27 PHE 0.021 0.002 PHE A 498 TYR 0.023 0.002 TYR B 60 ARG 0.004 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.757 Fit side-chains REVERT: A 77 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8243 (mm-40) REVERT: A 81 TYR cc_start: 0.8488 (t80) cc_final: 0.7758 (t80) REVERT: A 178 GLU cc_start: 0.7820 (tp30) cc_final: 0.7363 (mm-30) REVERT: A 192 GLU cc_start: 0.8219 (mp0) cc_final: 0.7618 (mp0) REVERT: A 201 ASP cc_start: 0.8599 (t0) cc_final: 0.8155 (t0) REVERT: A 203 TYR cc_start: 0.8667 (m-80) cc_final: 0.8254 (m-80) REVERT: A 332 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7305 (tt0) REVERT: A 412 PHE cc_start: 0.7835 (t80) cc_final: 0.7611 (t80) REVERT: A 422 MET cc_start: 0.8638 (tpp) cc_final: 0.8213 (tpp) REVERT: A 455 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7266 (mptt) REVERT: A 471 PHE cc_start: 0.8921 (m-10) cc_final: 0.8098 (t80) REVERT: B 32 ASN cc_start: 0.6781 (t0) cc_final: 0.6550 (t0) REVERT: B 60 TYR cc_start: 0.9020 (m-80) cc_final: 0.8685 (m-80) REVERT: C 128 ASN cc_start: 0.8374 (t0) cc_final: 0.7866 (t0) REVERT: C 161 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7716 (mm) outliers start: 29 outliers final: 27 residues processed: 155 average time/residue: 0.1491 time to fit residues: 30.1690 Evaluate side-chains 163 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5144 Z= 0.214 Angle : 0.728 18.948 6962 Z= 0.367 Chirality : 0.047 0.304 773 Planarity : 0.004 0.042 887 Dihedral : 5.760 81.630 724 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.66 % Allowed : 27.93 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.59 (0.33), residues: 649 helix: 2.17 (0.46), residues: 131 sheet: -0.10 (0.38), residues: 197 loop : -1.74 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 129 HIS 0.006 0.001 HIS A 27 PHE 0.022 0.001 PHE A 498 TYR 0.023 0.002 TYR B 60 ARG 0.002 0.000 ARG A 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8178 (mm-40) REVERT: A 81 TYR cc_start: 0.8422 (t80) cc_final: 0.8169 (t80) REVERT: A 178 GLU cc_start: 0.7953 (tp30) cc_final: 0.7742 (tp30) REVERT: A 192 GLU cc_start: 0.8127 (mp0) cc_final: 0.7556 (mp0) REVERT: A 201 ASP cc_start: 0.8570 (t0) cc_final: 0.8166 (t0) REVERT: A 203 TYR cc_start: 0.8636 (m-80) cc_final: 0.8187 (m-80) REVERT: A 341 LYS cc_start: 0.9128 (mttp) cc_final: 0.8724 (mttp) REVERT: A 412 PHE cc_start: 0.7824 (t80) cc_final: 0.7610 (t80) REVERT: A 422 MET cc_start: 0.8559 (tpp) cc_final: 0.8116 (tpp) REVERT: A 455 LYS cc_start: 0.7517 (ttmt) cc_final: 0.6860 (mptt) REVERT: A 471 PHE cc_start: 0.8871 (m-10) cc_final: 0.8022 (t80) REVERT: B 32 ASN cc_start: 0.6768 (t0) cc_final: 0.6539 (t0) REVERT: B 60 TYR cc_start: 0.8926 (m-80) cc_final: 0.8676 (m-80) REVERT: B 90 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.7623 (ptp-170) REVERT: C 128 ASN cc_start: 0.8303 (t0) cc_final: 0.7550 (t0) REVERT: C 161 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7844 (mm) outliers start: 25 outliers final: 23 residues processed: 154 average time/residue: 0.1604 time to fit residues: 31.9385 Evaluate side-chains 163 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123046 restraints weight = 7608.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127187 restraints weight = 4516.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130067 restraints weight = 3204.184| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 5144 Z= 0.337 Angle : 0.760 18.421 6962 Z= 0.391 Chirality : 0.049 0.318 773 Planarity : 0.004 0.043 887 Dihedral : 5.990 81.757 724 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.03 % Allowed : 27.93 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.79 (0.33), residues: 649 helix: 1.63 (0.45), residues: 137 sheet: -0.16 (0.37), residues: 197 loop : -1.80 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 129 HIS 0.006 0.001 HIS A 27 PHE 0.023 0.002 PHE A 498 TYR 0.022 0.002 TYR B 60 ARG 0.003 0.001 ARG A 2 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1472.04 seconds wall clock time: 27 minutes 21.90 seconds (1641.90 seconds total)