Starting phenix.real_space_refine on Fri Dec 8 06:06:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/12_2023/7uzu_26918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/12_2023/7uzu_26918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/12_2023/7uzu_26918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/12_2023/7uzu_26918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/12_2023/7uzu_26918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/12_2023/7uzu_26918.pdb" } resolution = 2.3 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= 0.283 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2286 2.51 5 N 677 2.21 5 O 766 1.98 5 H 3655 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 11": "OD1" <-> "OD2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 20": "OE1" <-> "OE2" Residue "W ASP 23": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7399 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 6920 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 18, 'TRANS': 432} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 399 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 78 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Conformer: "B" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O AHOH A1933 " occ=0.71 pdb=" O BHOH A1933 " occ=0.29 Time building chain proxies: 3.98, per 1000 atoms: 0.54 Number of scatterers: 7399 At special positions: 0 Unit cell: (94.62, 109.145, 59.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 766 8.00 N 677 7.00 C 2286 6.00 H 3655 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 Time building additional restraints: 7.04 Conformation dependent library (CDL) restraints added in 834.5 milliseconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 64.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 439 through 448 Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'W' and resid 4 through 7 Processing helix chain 'W' and resid 8 through 17 Processing helix chain 'W' and resid 18 through 22 191 hydrogen bonds defined for protein. 564 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: 2.66 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3650 1.03 - 1.23: 66 1.23 - 1.43: 1428 1.43 - 1.62: 2212 1.62 - 1.82: 25 Bond restraints: 7381 Sorted by residual: bond pdb=" C ASP A 196 " pdb=" N PRO A 197 " ideal model delta sigma weight residual 1.334 1.345 -0.011 8.40e-03 1.42e+04 1.76e+00 bond pdb=" CB LYS A 460 " pdb=" CG LYS A 460 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.59e-01 bond pdb=" CA THR A 393 " pdb=" CB THR A 393 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 1.526 1.535 -0.009 1.23e-02 6.61e+03 5.08e-01 bond pdb=" C ASP W 23 " pdb=" N PRO W 24 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.05e-01 ... (remaining 7376 not shown) Histogram of bond angle deviations from ideal: 100.25 - 106.48: 127 106.48 - 112.72: 8775 112.72 - 118.95: 1539 118.95 - 125.18: 2693 125.18 - 131.42: 251 Bond angle restraints: 13385 Sorted by residual: angle pdb=" CB MET W 11 " pdb=" CG MET W 11 " pdb=" SD MET W 11 " ideal model delta sigma weight residual 112.70 120.43 -7.73 3.00e+00 1.11e-01 6.65e+00 angle pdb=" C LYS A 436 " pdb=" N VAL A 437 " pdb=" CA VAL A 437 " ideal model delta sigma weight residual 121.97 117.64 4.33 1.80e+00 3.09e-01 5.78e+00 angle pdb=" OG1 THR A 393 " pdb=" CB THR A 393 " pdb=" CG2 THR A 393 " ideal model delta sigma weight residual 109.30 104.65 4.65 2.00e+00 2.50e-01 5.42e+00 angle pdb=" CG MET W 11 " pdb=" SD MET W 11 " pdb=" CE MET W 11 " ideal model delta sigma weight residual 100.90 105.55 -4.65 2.20e+00 2.07e-01 4.46e+00 angle pdb=" CB LYS A 460 " pdb=" CG LYS A 460 " pdb=" CD LYS A 460 " ideal model delta sigma weight residual 111.30 115.52 -4.22 2.30e+00 1.89e-01 3.37e+00 ... (remaining 13380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 2935 16.76 - 33.52: 302 33.52 - 50.27: 90 50.27 - 67.03: 25 67.03 - 83.79: 10 Dihedral angle restraints: 3362 sinusoidal: 1813 harmonic: 1549 Sorted by residual: dihedral pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" N LYS A 436 " pdb=" CA LYS A 436 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CG LYS A 380 " pdb=" CD LYS A 380 " pdb=" CE LYS A 380 " pdb=" NZ LYS A 380 " ideal model delta sinusoidal sigma weight residual -180.00 -122.66 -57.34 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB LYS A 460 " pdb=" CG LYS A 460 " pdb=" CD LYS A 460 " pdb=" CE LYS A 460 " ideal model delta sinusoidal sigma weight residual 60.00 116.45 -56.45 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 3359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 368 0.027 - 0.054: 144 0.054 - 0.080: 59 0.080 - 0.107: 24 0.107 - 0.134: 2 Chirality restraints: 597 Sorted by residual: chirality pdb=" CA ILE W 26 " pdb=" N ILE W 26 " pdb=" C ILE W 26 " pdb=" CB ILE W 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA PRO A 308 " pdb=" N PRO A 308 " pdb=" C PRO A 308 " pdb=" CB PRO A 308 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.92e-01 chirality pdb=" CA PRO A 364 " pdb=" N PRO A 364 " pdb=" C PRO A 364 " pdb=" CB PRO A 364 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 594 not shown) Planarity restraints: 1129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 18 " 0.176 9.50e-02 1.11e+02 5.89e-02 4.04e+00 pdb=" NE ARG A 18 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 18 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 18 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 18 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 18 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A 18 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 18 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 18 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 439 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 440 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 307 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 308 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.019 5.00e-02 4.00e+02 ... (remaining 1126 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 727 2.23 - 2.82: 16577 2.82 - 3.41: 21512 3.41 - 4.01: 29235 4.01 - 4.60: 43707 Nonbonded interactions: 111758 Sorted by model distance: nonbonded pdb=" HH TYR A 166 " pdb=" O GLY A 170 " model vdw 1.637 1.850 nonbonded pdb=" H GLY A 48 " pdb=" O HOH A1907 " model vdw 1.706 1.850 nonbonded pdb=" HZ1 LYS A 380 " pdb=" O SER W 29 " model vdw 1.727 1.850 nonbonded pdb=" HH TYR W 21 " pdb=" O HOH W1001 " model vdw 1.734 1.850 nonbonded pdb=" O ALA A 181 " pdb="HD22 ASN A 218 " model vdw 1.747 1.850 ... (remaining 111753 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=0.29 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.130 Extract box with map and model: 5.530 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.060 Find NCS groups from input model: 0.140 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3726 Z= 0.201 Angle : 0.568 7.734 5061 Z= 0.295 Chirality : 0.036 0.134 597 Planarity : 0.005 0.077 668 Dihedral : 17.468 83.789 1365 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.52 % Allowed : 16.80 % Favored : 82.69 % 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: 1.73 (0.39), residues: 479 helix: 1.75 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.03 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 350 PHE 0.009 0.001 PHE A 234 TYR 0.013 0.002 TYR A 455 ARG 0.008 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.611 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 2.7692 time to fit residues: 190.9999 Evaluate side-chains 66 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.134 Angle : 0.470 4.884 5061 Z= 0.242 Chirality : 0.035 0.129 597 Planarity : 0.004 0.040 668 Dihedral : 4.004 24.176 509 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.03 % Allowed : 15.50 % Favored : 83.46 % 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: 2.29 (0.40), residues: 479 helix: 2.15 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.30 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.006 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.005 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.646 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 72 average time/residue: 2.7565 time to fit residues: 204.3479 Evaluate side-chains 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3726 Z= 0.209 Angle : 0.502 4.364 5061 Z= 0.264 Chirality : 0.037 0.130 597 Planarity : 0.004 0.047 668 Dihedral : 4.238 24.821 509 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.03 % Allowed : 15.76 % Favored : 83.20 % 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: 2.22 (0.40), residues: 479 helix: 2.08 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.31 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 343 PHE 0.010 0.001 PHE A 234 TYR 0.011 0.002 TYR A 455 ARG 0.004 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.631 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 2.6736 time to fit residues: 195.7323 Evaluate side-chains 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.160 Angle : 0.473 4.380 5061 Z= 0.247 Chirality : 0.036 0.129 597 Planarity : 0.004 0.050 668 Dihedral : 4.111 24.625 509 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.29 % Allowed : 15.50 % Favored : 83.20 % 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: 2.41 (0.40), residues: 479 helix: 2.21 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.42 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.008 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.005 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.681 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 2.7796 time to fit residues: 206.2107 Evaluate side-chains 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 2.5720 time to fit residues: 3.4585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3726 Z= 0.224 Angle : 0.510 4.443 5061 Z= 0.270 Chirality : 0.038 0.129 597 Planarity : 0.005 0.056 668 Dihedral : 4.317 24.961 509 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.81 % Allowed : 14.73 % Favored : 83.46 % 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: 2.20 (0.39), residues: 479 helix: 2.06 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.32 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 343 PHE 0.010 0.001 PHE A 234 TYR 0.011 0.003 TYR A 455 ARG 0.004 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.627 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 2.7377 time to fit residues: 209.0168 Evaluate side-chains 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.7931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3726 Z= 0.196 Angle : 0.498 4.557 5061 Z= 0.262 Chirality : 0.037 0.130 597 Planarity : 0.004 0.044 668 Dihedral : 4.261 24.914 509 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.29 % Allowed : 16.28 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.39), residues: 479 helix: 2.11 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.35 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 343 PHE 0.009 0.001 PHE A 234 TYR 0.012 0.002 TYR A 455 ARG 0.003 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.610 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 2.7217 time to fit residues: 202.0881 Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.7494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.143 Angle : 0.467 4.362 5061 Z= 0.243 Chirality : 0.035 0.131 597 Planarity : 0.004 0.061 668 Dihedral : 4.042 24.448 509 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.81 % Allowed : 15.76 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.40), residues: 479 helix: 2.31 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.47 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 244 PHE 0.007 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.007 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.619 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 2.6979 time to fit residues: 203.3653 Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.8141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3726 Z= 0.173 Angle : 0.481 4.389 5061 Z= 0.253 Chirality : 0.036 0.131 597 Planarity : 0.004 0.062 668 Dihedral : 4.117 24.465 509 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.81 % Allowed : 15.76 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.40), residues: 479 helix: 2.25 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.46 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 343 PHE 0.009 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.006 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.582 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 2.6743 time to fit residues: 203.9884 Evaluate side-chains 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 42 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.132 Angle : 0.457 4.348 5061 Z= 0.238 Chirality : 0.035 0.130 597 Planarity : 0.004 0.056 668 Dihedral : 3.912 23.998 509 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.29 % Allowed : 16.28 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.40), residues: 479 helix: 2.41 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.58 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 PHE 0.006 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.006 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.601 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 2.6264 time to fit residues: 194.8976 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 2.3453 time to fit residues: 3.1650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 10 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 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.131 Angle : 0.460 5.260 5061 Z= 0.237 Chirality : 0.035 0.130 597 Planarity : 0.004 0.054 668 Dihedral : 3.825 23.456 509 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.03 % Allowed : 16.28 % Favored : 82.69 % 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: 2.79 (0.40), residues: 479 helix: 2.47 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.65 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 PHE 0.006 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.006 0.000 ARG A 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.619 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 72 average time/residue: 2.6125 time to fit residues: 194.1236 Evaluate side-chains 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.7690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.0270 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113277 restraints weight = 10534.183| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.22 r_work: 0.3104 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.128 Angle : 0.454 5.218 5061 Z= 0.233 Chirality : 0.034 0.130 597 Planarity : 0.004 0.053 668 Dihedral : 3.754 23.069 509 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.03 % Allowed : 15.50 % Favored : 83.46 % 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: 2.85 (0.40), residues: 479 helix: 2.51 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.67 (0.57), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 PHE 0.006 0.001 PHE A 234 TYR 0.006 0.001 TYR W 8 ARG 0.006 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4838.95 seconds wall clock time: 84 minutes 49.68 seconds (5089.68 seconds total)