Starting phenix.real_space_refine on Thu Jan 18 02:03:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/01_2024/7uzu_26918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/01_2024/7uzu_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_26918/01_2024/7uzu_26918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/01_2024/7uzu_26918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/01_2024/7uzu_26918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzu_26918/01_2024/7uzu_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-1.21-5211/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: 3.89, per 1000 atoms: 0.53 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: 6.19 Conformation dependent library (CDL) restraints added in 755.1 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: 0.56 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: 2.51 Time building geometry restraints manager: 6.39 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: 2966 16.76 - 33.52: 302 33.52 - 50.27: 90 50.27 - 67.03: 25 67.03 - 83.79: 10 Dihedral angle restraints: 3393 sinusoidal: 1844 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 3390 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: 1.030 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: 5.320 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 28.280 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.350 ------------------------------------------------------------------------------- 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 : 0.604 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 2.5862 time to fit residues: 178.5386 Evaluate side-chains 66 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE 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: 5.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 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: 0.8584 moved from start: 0.0472 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= 0.154 Angle : 0.484 4.958 5061 Z= 0.250 Chirality : 0.035 0.129 597 Planarity : 0.004 0.042 668 Dihedral : 4.450 37.613 511 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.69 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: 2.19 (0.39), residues: 479 helix: 2.08 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.25 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.007 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.004 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 75 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.604 Fit side-chains REVERT: A 311 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8912 (mtt) outliers start: 5 outliers final: 0 residues processed: 73 average time/residue: 2.6272 time to fit residues: 197.6155 Evaluate side-chains 69 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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: 0.8582 moved from start: 0.0607 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= 0.152 Angle : 0.467 4.310 5061 Z= 0.243 Chirality : 0.035 0.129 597 Planarity : 0.004 0.046 668 Dihedral : 4.034 24.380 509 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.83 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: 2.43 (0.40), residues: 479 helix: 2.24 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.39 (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 0.009 0.002 TYR A 455 ARG 0.006 0.000 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 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.561 Fit side-chains REVERT: A 91 ASP cc_start: 0.8152 (m-30) cc_final: 0.7852 (m-30) REVERT: A 196 ASP cc_start: 0.7691 (t70) cc_final: 0.7296 (t70) REVERT: A 311 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8908 (mtt) outliers start: 4 outliers final: 1 residues processed: 70 average time/residue: 2.6461 time to fit residues: 190.9390 Evaluate side-chains 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET 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: 2.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8603 moved from start: 0.0637 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= 0.213 Angle : 0.500 4.436 5061 Z= 0.264 Chirality : 0.037 0.129 597 Planarity : 0.004 0.051 668 Dihedral : 4.248 24.798 509 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.42 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: 2.26 (0.40), residues: 479 helix: 2.11 (0.28), 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 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: 4 poor density : 70 time to evaluate : 0.603 Fit side-chains REVERT: A 91 ASP cc_start: 0.8159 (m-30) cc_final: 0.7850 (m-30) REVERT: A 196 ASP cc_start: 0.7707 (t70) cc_final: 0.7322 (t70) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 2.5963 time to fit residues: 195.1779 Evaluate side-chains 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS 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: 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: 5.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0666 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= 0.182 Angle : 0.490 4.351 5061 Z= 0.257 Chirality : 0.036 0.129 597 Planarity : 0.004 0.038 668 Dihedral : 4.183 24.769 509 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.55 % Allowed : 15.50 % 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: 2.35 (0.40), residues: 479 helix: 2.18 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.36 (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 0.011 0.002 TYR A 455 ARG 0.003 0.000 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 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.656 Fit side-chains REVERT: A 91 ASP cc_start: 0.8154 (m-30) cc_final: 0.7856 (m-30) REVERT: A 196 ASP cc_start: 0.7672 (t70) cc_final: 0.7291 (t70) REVERT: A 311 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8915 (mtt) outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 2.6708 time to fit residues: 198.1035 Evaluate side-chains 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.8591 moved from start: 0.0710 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= 0.167 Angle : 0.479 4.401 5061 Z= 0.251 Chirality : 0.036 0.128 597 Planarity : 0.004 0.058 668 Dihedral : 4.126 24.623 509 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.55 % Allowed : 15.76 % 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: 2.43 (0.40), residues: 479 helix: 2.24 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.41 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 343 PHE 0.008 0.001 PHE A 234 TYR 0.011 0.002 TYR A 455 ARG 0.006 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 75 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.624 Fit side-chains REVERT: A 91 ASP cc_start: 0.8145 (m-30) cc_final: 0.7855 (m-30) REVERT: A 196 ASP cc_start: 0.7671 (t70) cc_final: 0.7295 (t70) REVERT: A 311 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8909 (mtt) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 2.4445 time to fit residues: 183.8953 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS 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: 6.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.8562 moved from start: 0.0830 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= 0.125 Angle : 0.449 4.355 5061 Z= 0.232 Chirality : 0.034 0.129 597 Planarity : 0.004 0.058 668 Dihedral : 3.856 23.946 509 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.55 % Allowed : 16.28 % Favored : 82.17 % 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: 2.73 (0.40), residues: 479 helix: 2.45 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.57 (0.57), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 83 PHE 0.005 0.001 PHE A 234 TYR 0.008 0.001 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 76 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.612 Fit side-chains REVERT: A 91 ASP cc_start: 0.8115 (m-30) cc_final: 0.7846 (m-30) REVERT: A 196 ASP cc_start: 0.7626 (t70) cc_final: 0.7258 (t70) REVERT: A 311 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8939 (mtt) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 2.4999 time to fit residues: 191.0214 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.8587 moved from start: 0.0770 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= 0.174 Angle : 0.479 4.389 5061 Z= 0.250 Chirality : 0.036 0.130 597 Planarity : 0.004 0.061 668 Dihedral : 4.019 24.118 509 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.29 % Allowed : 16.80 % 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: 2.57 (0.40), residues: 479 helix: 2.32 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.51 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 343 PHE 0.008 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 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.611 Fit side-chains REVERT: A 91 ASP cc_start: 0.8136 (m-30) cc_final: 0.7868 (m-30) REVERT: A 196 ASP cc_start: 0.7673 (t70) cc_final: 0.7290 (t70) REVERT: A 311 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8911 (mtt) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 2.6120 time to fit residues: 191.0793 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8581 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 0.020 3726 Z= 0.156 Angle : 0.475 5.324 5061 Z= 0.246 Chirality : 0.035 0.130 597 Planarity : 0.004 0.064 668 Dihedral : 3.981 24.023 509 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.29 % Allowed : 16.80 % 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: 2.62 (0.40), residues: 479 helix: 2.35 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.55 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 343 PHE 0.008 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.007 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 74 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.520 Fit side-chains REVERT: A 91 ASP cc_start: 0.8135 (m-30) cc_final: 0.7870 (m-30) REVERT: A 196 ASP cc_start: 0.7655 (t70) cc_final: 0.7270 (t70) REVERT: A 311 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8948 (mtt) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 2.4469 time to fit residues: 181.5979 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8577 moved from start: 0.0836 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= 0.148 Angle : 0.467 4.379 5061 Z= 0.243 Chirality : 0.035 0.131 597 Planarity : 0.004 0.061 668 Dihedral : 3.932 23.775 509 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.55 % Allowed : 15.76 % 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: 2.68 (0.40), residues: 479 helix: 2.38 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.60 (0.57), 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 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 74 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.441 Fit side-chains REVERT: A 91 ASP cc_start: 0.8127 (m-30) cc_final: 0.7861 (m-30) REVERT: A 125 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: A 196 ASP cc_start: 0.7645 (t70) cc_final: 0.7265 (t70) REVERT: A 311 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8948 (mtt) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 2.4087 time to fit residues: 176.0396 Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 0.0020 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.131023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112823 restraints weight = 10589.445| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.23 r_work: 0.3075 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0879 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= 0.133 Angle : 0.458 4.654 5061 Z= 0.236 Chirality : 0.035 0.130 597 Planarity : 0.004 0.059 668 Dihedral : 3.827 23.420 509 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.29 % Allowed : 15.76 % 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: 2.78 (0.40), residues: 479 helix: 2.45 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.65 (0.57), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.006 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.007 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.49 seconds wall clock time: 90 minutes 12.73 seconds (5412.73 seconds total)