Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 22:34:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/07_2023/6zqi_11364.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/07_2023/6zqi_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_11364/07_2023/6zqi_11364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/07_2023/6zqi_11364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/07_2023/6zqi_11364.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqi_11364/07_2023/6zqi_11364.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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 chiralities: 1 Time building chain proxies: 3.25, per 1000 atoms: 0.65 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: 1.99 Conformation dependent library (CDL) restraints added in 773.8 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: 0.37 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: 1.45 Time building geometry restraints manager: 2.17 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: 2799 17.87 - 35.75: 188 35.75 - 53.62: 37 53.62 - 71.50: 6 71.50 - 89.37: 5 Dihedral angle restraints: 3035 sinusoidal: 1182 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 3032 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: 0.180 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: 1.070 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 17.930 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- 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 : 12.413 89.370 1826 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 % 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 *********************** 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 : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 192 average time/residue: 0.1982 time to fit residues: 46.5559 Evaluate side-chains 143 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0573 time to fit residues: 0.9084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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: 0.7721 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 5144 Z= 0.220 Angle : 0.638 15.084 6962 Z= 0.329 Chirality : 0.046 0.288 773 Planarity : 0.004 0.034 887 Dihedral : 4.917 78.413 701 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 4.10 % 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: 1.29 (0.46), residues: 131 sheet: -0.26 (0.36), residues: 194 loop : -2.17 (0.29), residues: 324 *********************** 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 177 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.594 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 164 average time/residue: 0.1738 time to fit residues: 36.5730 Evaluate side-chains 154 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0516 time to fit residues: 2.1513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 5144 Z= 0.262 Angle : 0.663 19.149 6962 Z= 0.342 Chirality : 0.046 0.308 773 Planarity : 0.004 0.039 887 Dihedral : 5.183 80.160 701 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.31), residues: 649 helix: 1.57 (0.46), residues: 132 sheet: -0.23 (0.36), residues: 191 loop : -1.95 (0.30), residues: 326 *********************** 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 156 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 154 average time/residue: 0.1625 time to fit residues: 32.3543 Evaluate side-chains 139 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0490 time to fit residues: 1.0379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 30 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 0.0670 chunk 59 optimal weight: 0.0570 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 ASN ** 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: 0.7713 moved from start: 0.2945 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= 0.143 Angle : 0.592 12.876 6962 Z= 0.305 Chirality : 0.044 0.198 773 Planarity : 0.003 0.037 887 Dihedral : 4.972 81.483 701 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 4.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.33), residues: 649 helix: 2.22 (0.49), residues: 126 sheet: 0.18 (0.37), residues: 197 loop : -1.80 (0.30), residues: 326 *********************** 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 171 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 164 average time/residue: 0.1541 time to fit residues: 32.8762 Evaluate side-chains 147 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0533 time to fit residues: 2.0297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 5144 Z= 0.275 Angle : 0.673 20.774 6962 Z= 0.349 Chirality : 0.047 0.315 773 Planarity : 0.004 0.040 887 Dihedral : 5.196 80.062 701 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 2.98 % 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: -0.72 (0.32), residues: 649 helix: 2.06 (0.46), residues: 130 sheet: -0.11 (0.37), residues: 192 loop : -1.84 (0.31), residues: 327 *********************** 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 160 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.599 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 152 average time/residue: 0.1671 time to fit residues: 32.7055 Evaluate side-chains 139 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0822 time to fit residues: 1.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.0470 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.0670 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN ** 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: 0.7742 moved from start: 0.3349 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= 0.153 Angle : 0.627 15.302 6962 Z= 0.323 Chirality : 0.045 0.257 773 Planarity : 0.003 0.038 887 Dihedral : 5.034 82.754 701 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 2.23 % 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: -0.47 (0.33), residues: 649 helix: 2.27 (0.48), residues: 131 sheet: 0.10 (0.38), residues: 188 loop : -1.72 (0.31), residues: 330 *********************** 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 155 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.656 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 147 average time/residue: 0.1637 time to fit residues: 31.2577 Evaluate side-chains 142 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0532 time to fit residues: 1.3375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 39 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** 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: 0.7822 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 5144 Z= 0.282 Angle : 0.729 23.142 6962 Z= 0.376 Chirality : 0.049 0.345 773 Planarity : 0.004 0.040 887 Dihedral : 5.382 81.741 701 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 1.86 % 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: -0.58 (0.32), residues: 649 helix: 1.99 (0.46), residues: 131 sheet: 0.02 (0.37), residues: 192 loop : -1.70 (0.32), residues: 326 *********************** 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 151 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 0.635 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 147 average time/residue: 0.1627 time to fit residues: 31.0536 Evaluate side-chains 137 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0475 time to fit residues: 1.1942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 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 32 ASN ** 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: 0.7815 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 5144 Z= 0.243 Angle : 0.714 18.413 6962 Z= 0.366 Chirality : 0.048 0.310 773 Planarity : 0.004 0.040 887 Dihedral : 5.447 82.296 701 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 1.49 % 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: -0.52 (0.33), residues: 649 helix: 2.10 (0.46), residues: 131 sheet: 0.05 (0.37), residues: 192 loop : -1.69 (0.32), residues: 326 *********************** 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 143 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.618 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 139 average time/residue: 0.1685 time to fit residues: 30.2687 Evaluate side-chains 137 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0560 time to fit residues: 1.3979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 227 HIS ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 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: 0.7871 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 5144 Z= 0.374 Angle : 0.804 20.051 6962 Z= 0.414 Chirality : 0.051 0.341 773 Planarity : 0.004 0.042 887 Dihedral : 5.753 80.129 701 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 1.68 % 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: -0.82 (0.33), residues: 649 helix: 1.57 (0.45), residues: 136 sheet: -0.17 (0.37), residues: 202 loop : -1.82 (0.33), residues: 311 *********************** 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 146 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.620 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.1687 time to fit residues: 30.6215 Evaluate side-chains 142 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0497 time to fit residues: 1.4308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 32 ASN ** 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: 0.7802 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5144 Z= 0.193 Angle : 0.722 19.104 6962 Z= 0.368 Chirality : 0.049 0.301 773 Planarity : 0.004 0.040 887 Dihedral : 5.477 81.483 701 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.74 % 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: -0.52 (0.33), residues: 649 helix: 2.24 (0.48), residues: 131 sheet: -0.02 (0.38), residues: 187 loop : -1.69 (0.31), residues: 331 ********************** 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 146 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 0.651 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 142 average time/residue: 0.1901 time to fit residues: 34.8798 Evaluate side-chains 140 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0489 time to fit residues: 1.1387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** 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 = 0.3897 r_free = 0.3897 target = 0.159532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128397 restraints weight = 7423.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132601 restraints weight = 4381.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135586 restraints weight = 3098.632| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5144 Z= 0.204 Angle : 0.741 18.212 6962 Z= 0.372 Chirality : 0.047 0.288 773 Planarity : 0.004 0.048 887 Dihedral : 5.394 81.984 701 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.37 % 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: -0.46 (0.33), residues: 649 helix: 2.40 (0.48), residues: 131 sheet: 0.03 (0.38), residues: 192 loop : -1.73 (0.32), residues: 326 =============================================================================== Job complete usr+sys time: 1413.04 seconds wall clock time: 26 minutes 13.82 seconds (1573.82 seconds total)