Starting phenix.real_space_refine on Tue Nov 14 03:50:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/11_2023/7uzu_26918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/11_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_26918/11_2023/7uzu_26918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/11_2023/7uzu_26918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/11_2023/7uzu_26918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/11_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-1.21rc1-5144/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: 3.96, 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: 6.86 Conformation dependent library (CDL) restraints added in 815.0 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: 0.52 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: 2.40 Time building geometry restraints manager: 7.05 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: 2523 16.76 - 33.52: 289 33.52 - 50.27: 77 50.27 - 67.03: 24 67.03 - 83.79: 10 Dihedral angle restraints: 2923 sinusoidal: 1374 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 2920 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: 1.270 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: 0.120 Extract box with map and model: 5.420 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 29.200 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.110 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.698 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 2.7641 time to fit residues: 190.7824 Evaluate side-chains 66 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7968 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.8583 moved from start: 0.0484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3726 Z= 0.153 Angle : 0.485 4.944 5061 Z= 0.250 Chirality : 0.035 0.130 597 Planarity : 0.004 0.041 668 Dihedral : 4.114 24.460 509 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.29 % Allowed : 15.25 % 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: 2.21 (0.40), residues: 479 helix: 2.08 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.26 (0.55), residues: 159 *********************** 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 75 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.674 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 73 average time/residue: 2.7879 time to fit residues: 209.5774 Evaluate side-chains 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7622 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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: 0.8575 moved from start: 0.0639 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= 0.142 Angle : 0.463 4.344 5061 Z= 0.239 Chirality : 0.035 0.130 597 Planarity : 0.004 0.045 668 Dihedral : 3.971 24.193 509 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.52 % Allowed : 15.76 % Favored : 83.72 % 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: 2.49 (0.40), residues: 479 helix: 2.29 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.40 (0.56), residues: 159 *********************** 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 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.659 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 2.6597 time to fit residues: 189.1751 Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7092 ------------------------------------------------------------------------------- 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: 0.8980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.8588 moved from start: 0.0657 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= 0.169 Angle : 0.476 4.378 5061 Z= 0.248 Chirality : 0.036 0.129 597 Planarity : 0.004 0.050 668 Dihedral : 4.072 24.271 509 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.78 % Allowed : 15.50 % Favored : 83.72 % 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: 2.45 (0.40), residues: 479 helix: 2.25 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.41 (0.56), residues: 159 *********************** 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 72 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.605 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 2.7980 time to fit residues: 204.5913 Evaluate side-chains 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7783 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 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: 0.7980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3726 Z= 0.153 Angle : 0.467 4.361 5061 Z= 0.243 Chirality : 0.035 0.129 597 Planarity : 0.004 0.052 668 Dihedral : 4.027 24.230 509 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.29 % Allowed : 15.25 % 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: 2.53 (0.40), residues: 479 helix: 2.31 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.44 (0.56), residues: 159 *********************** 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 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.593 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 2.7839 time to fit residues: 206.3442 Evaluate side-chains 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 2.4956 time to fit residues: 3.3353 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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: 0.8614 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3726 Z= 0.265 Angle : 0.533 4.492 5061 Z= 0.283 Chirality : 0.039 0.130 597 Planarity : 0.005 0.060 668 Dihedral : 4.399 25.097 509 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.29 % Allowed : 14.99 % Favored : 83.72 % 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: 2.15 (0.39), residues: 479 helix: 2.02 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.28 (0.55), residues: 159 *********************** 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 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.552 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 2.6239 time to fit residues: 192.1695 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: 0.7657 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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** A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3726 Z= 0.139 Angle : 0.467 4.398 5061 Z= 0.242 Chirality : 0.035 0.130 597 Planarity : 0.004 0.048 668 Dihedral : 4.048 24.451 509 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 16.54 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.40), residues: 479 helix: 2.30 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.45 (0.56), residues: 159 *********************** 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: 6 poor density : 68 time to evaluate : 0.679 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 2.6496 time to fit residues: 196.8619 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 2.4895 time to fit residues: 3.3268 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.8583 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3726 Z= 0.156 Angle : 0.476 4.436 5061 Z= 0.247 Chirality : 0.035 0.130 597 Planarity : 0.004 0.062 668 Dihedral : 4.043 24.242 509 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.03 % Allowed : 16.54 % 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: 2.30 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.49 (0.56), residues: 159 *********************** 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 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.620 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 2.7126 time to fit residues: 201.3372 Evaluate side-chains 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7110 ------------------------------------------------------------------------------- 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: 0.8980 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8584 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3726 Z= 0.158 Angle : 0.475 4.448 5061 Z= 0.248 Chirality : 0.036 0.130 597 Planarity : 0.004 0.063 668 Dihedral : 4.046 24.169 509 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.83 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: 2.55 (0.40), residues: 479 helix: 2.30 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.50 (0.56), residues: 159 *********************** 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 : 0.642 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 2.6184 time to fit residues: 194.4558 Evaluate side-chains 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.7945 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8561 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3726 Z= 0.127 Angle : 0.461 4.353 5061 Z= 0.237 Chirality : 0.035 0.130 597 Planarity : 0.004 0.060 668 Dihedral : 3.844 23.598 509 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.78 % Allowed : 16.80 % 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: 2.75 (0.40), residues: 479 helix: 2.44 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.63 (0.57), residues: 159 ********************** 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 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.668 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 71 average time/residue: 2.6584 time to fit residues: 194.5970 Evaluate side-chains 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7592 ------------------------------------------------------------------------------- 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: 0.0970 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.130441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112617 restraints weight = 10605.281| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.20 r_work: 0.3044 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 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 = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3726 Z= 0.200 Angle : 0.505 4.606 5061 Z= 0.264 Chirality : 0.037 0.130 597 Planarity : 0.004 0.060 668 Dihedral : 4.131 24.065 509 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.03 % Allowed : 16.02 % Favored : 82.95 % 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: 2.44 (0.40), residues: 479 helix: 2.22 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.47 (0.56), residues: 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4686.67 seconds wall clock time: 82 minutes 8.94 seconds (4928.94 seconds total)